integration details

@@ -1200,11 +1200,13 @@ class Pipeline:
         # Check for a list of known problems:
         if os.path.isfile(runDir + "/known_issues.txt"):
             with open(runDir + "/known_issues.txt", 'r') as issues:
-                self.known_issues = [x[:-1] for x in issues.readlines()]
+                if self.HOMOLOGY:
+                    self.known_issues = [ x[:-1] for x in issues.readlines() if '-' in x ]
+                else:
+                    self.known_issues = [ x[:-1] for x in issues.readlines() id not '-' in x ]
             if self.USE_KNOWN_ISSUES:
                 print("\t> Ignoring known issues:")
-                for x in self.known_issues:
-                    print("\t  ", x)
+                print(" ".join(self.known_issues")
 
         if self.HOMOLOGY:
             # Ask Rfam if some are mapped to Rfam families
@@ -1560,6 +1562,7 @@ class Pipeline:
         if self.ARCHIVE:
             os.makedirs(runDir + "/archive", exist_ok=True)
             datestr = time.strftime('%Y%m%d')
+            subprocess.run(["rm", "-f", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"])
             subprocess.run(["tar", "-C", path_to_3D_data + "/datapoints", "-czf", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", "."])
             subprocess.run(["ln", "-s", runDir + f"/archive/RNANET_datapoints_{datestr}.tar.gz", runDir + f"/archive/RNANET_datapoints_latest.tar.gz"])
 

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+6xqe_1_2X
+6xz7_1_F
+6xz7_1_G
+6y69_1_W
+6ybv_1_K
+6ybv_1_W
+6ys3_1_A
+6ys3_1_B
+6ys3_1_V
+6ysr_1_W
+6yss_1_W
+6yst_1_W
+6ysu_1_W
+6yud_1_K
+6yud_1_M
+6yud_1_O
+6yud_1_P
+6yud_1_Q
 6ywo_1_E
-6ywo_1_K
-6vm6_1_I
-6vm6_1_H
+6ywo_1_F
 6ywo_1_I
-2a1r_1_C
-2a1r_1_D
-3gpq_1_E
-3gpq_1_F
-6o79_1_C
-6vm6_1_K
-6hyu_1_D
-1laj_1_R
-6ybv_1_K
-6mpf_1_W
-6spc_1_A
-6spe_1_A
-6fti_1_V
-6ftj_1_V
-6ftg_1_V
-4g0a_1_G
-4g0a_1_F
-4g0a_1_E
-2b2d_1_S
-5hkc_1_C
-1rmv_1_B
-4qu7_1_X
-4qu7_1_V
-4qu7_1_U
-4v5z_1_AH
-4v5z_1_AA
-4v5z_1_AB
-4v5z_1_AC
-4v5z_1_AD
-4v5z_1_AE
-4v5z_1_AF
-4v5z_1_AG
-6pmi_1_3
-6pmj_1_3
-5hjz_1_C
+6ywo_1_K
+6z1p_1_AA
+6z1p_1_AB
+6z1p_1_BA
+6z1p_1_BB
+6z8k_1_X
+6zmw_1_W
+6zvh_1_X
+6zvi_1_D
+6zvi_1_E
+6zvi_1_H
+7jql_1_1X
+7jql_1_2X
+7jqm_1_1X
+7jqm_1_2X
+7jyy_1_E
+7jyy_1_F
+7jz0_1_E
+7jz0_1_F
+7k00_1_5
+7k00_1_B

-1eg0_1_O_1-73
-DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_O_1-73.
-
-2rdo_1_A_3-118
-DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_A_3-118.
-
-4v48_1_A9_3-118
-DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A9_3-118.
-
-4v47_1_A9_3-118
-DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A9_3-118.
-
-1vy7_1_AY_1-73
-Sequence is too short. (< 5 resolved nts)
-
-1vy7_1_CY_1-73
-Sequence is too short. (< 5 resolved nts)
-
-4w2h_1_CY_1-73
-Sequence is too short. (< 5 resolved nts)
-
-1jgq_1_A_2-1520
-Could not find nucleotides of chain A in annotation 1jgq.json. Either there is a problem with 1jgq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
-
-4v42_1_AA_2-1520
-Could not find nucleotides of chain AA in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
-
-1jgo_1_A_2-1520
-Could not find nucleotides of chain A in annotation 1jgo.json. Either there is a problem with 1jgo mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
-
-1jgp_1_A_2-1520
-Could not find nucleotides of chain A in annotation 1jgp.json. Either there is a problem with 1jgp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
-
-1ml5_1_A_2-1520
-Could not find nucleotides of chain A in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
-
-4v42_1_BA_1-2914
-Could not find nucleotides of chain BA in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
-
-1ml5_1_a_1-2914
-Could not find nucleotides of chain a in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
-
-4v42_1_BB_5-121
-Could not find nucleotides of chain BB in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
-
 1ml5_1_b_5-121
 Could not find nucleotides of chain b in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
-2rdo_1_B_1-2904
-DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_1-2904.
-
-4v48_1_A0_1-2904
-DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_1-2904.
-
-4v47_1_A0_1-2904
-DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_1-2904.
+1ml5_1_a_1-2914
+Could not find nucleotides of chain a in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
-4v48_1_BA_1-1543
-DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA_1-1543.
+1ml5_1_A_2-1520
+Could not find nucleotides of chain A in annotation 1ml5.json. Either there is a problem with 1ml5 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
-4v47_1_BA_1-1542
-DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA_1-1542.
+2z9q_1_A_1-72
+DSSR warning 2z9q.json: no nucleotides found. Ignoring 2z9q_1_A_1-72.
 
 1ls2_1_B_1-73
 DSSR warning 1ls2.json: no nucleotides found. Ignoring 1ls2_1_B_1-73.
@@ -73,15 +22,33 @@ DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_Y_1-72.
 4v48_1_A6_1-73
 DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A6_1-73.
 
-2z9q_1_A_1-72
-DSSR warning 2z9q.json: no nucleotides found. Ignoring 2z9q_1_A_1-72.
-
 1gsg_1_T_1-72
 DSSR warning 1gsg.json: no nucleotides found. Ignoring 1gsg_1_T_1-72.
 
 3jcr_1_H_1-115
 DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_H_1-115.
 
+1vy7_1_AY_1-73
+Sequence is too short. (< 5 resolved nts)
+
+1vy7_1_CY_1-73
+Sequence is too short. (< 5 resolved nts)
+
+4w2h_1_CY_1-73
+Sequence is too short. (< 5 resolved nts)
+
+2rdo_1_A_3-118
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_A_3-118.
+
+4v48_1_A9_3-118
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A9_3-118.
+
+4v47_1_A9_3-118
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A9_3-118.
+
+2ob7_1_A_10-319
+DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_A_10-319.
+
 1x1l_1_A_1-132
 DSSR warning 1x1l.json: no nucleotides found. Ignoring 1x1l_1_A_1-132.
 
@@ -91,8 +58,20 @@ DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_Z_1-93.
 2ob7_1_D_1-132
 DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_D_1-132.
 
-2ob7_1_A_10-319
-DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_A_10-319.
+4v42_1_BB_5-121
+Could not find nucleotides of chain BB in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
+4v42_1_BA_1-2914
+Could not find nucleotides of chain BA in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
+2rdo_1_B_1-2904
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_1-2904.
+
+4v48_1_A0_1-2904
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_1-2904.
+
+4v47_1_A0_1-2904
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_1-2904.
 
 1r2x_1_C_1-58
 DSSR warning 1r2x.json: no nucleotides found. Ignoring 1r2x_1_C_1-58.
@@ -103,9 +82,18 @@ DSSR warning 1r2w.json: no nucleotides found. Ignoring 1r2w_1_C_1-58.
 1eg0_1_L_1-56
 DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_L_1-56.
 
+4v48_1_BA_1-1543
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA_1-1543.
+
+4v47_1_BA_1-1542
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA_1-1542.
+
 1zc8_1_A_1-59
 DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_A_1-59.
 
+1eg0_1_O_1-73
+DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_O_1-73.
+
 1mvr_1_D_1-61
 DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_D_1-61.
 
@@ -115,6 +103,18 @@ DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_9_1-123.
 1zn1_1_B_1-59
 DSSR warning 1zn1.json: no nucleotides found. Ignoring 1zn1_1_B_1-59.
 
+1jgq_1_A_2-1520
+Could not find nucleotides of chain A in annotation 1jgq.json. Either there is a problem with 1jgq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
+4v42_1_AA_2-1520
+Could not find nucleotides of chain AA in annotation 4v42.json. Either there is a problem with 4v42 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
+1jgo_1_A_2-1520
+Could not find nucleotides of chain A in annotation 1jgo.json. Either there is a problem with 1jgo mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
+1jgp_1_A_2-1520
+Could not find nucleotides of chain A in annotation 1jgp.json. Either there is a problem with 1jgp mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
 1emi_1_B_1-108
 DSSR warning 1emi.json: no nucleotides found. Ignoring 1emi_1_B_1-108.
 
@@ -583,6 +583,9 @@ Could not find nucleotides of chain U in annotation 6lkq.json. Either there is a
 7k00_1_B
 Could not find nucleotides of chain B in annotation 7k00.json. Either there is a problem with 7k00 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
+6ys3_1_A
+Could not find nucleotides of chain A in annotation 6ys3.json. Either there is a problem with 6ys3 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
 6qdw_1_A
 Could not find nucleotides of chain A in annotation 6qdw.json. Either there is a problem with 6qdw mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
@@ -1000,6 +1003,9 @@ Sequence is too short. (< 5 resolved nts)
 6lkq_1_T
 Could not find nucleotides of chain T in annotation 6lkq.json. Either there is a problem with 6lkq mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
+6ys3_1_B
+Could not find nucleotides of chain B in annotation 6ys3.json. Either there is a problem with 6ys3 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
 6qdw_1_B
 Could not find nucleotides of chain B in annotation 6qdw.json. Either there is a problem with 6qdw mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
@@ -1379,7 +1385,7 @@ Sequence is too short. (< 5 resolved nts)
 Sequence is too short. (< 5 resolved nts)
 
 1cwp_1_E
-Could not download and/or find annotations for 1cwp_1_E.
+Sequence is too short. (< 5 resolved nts)
 
 6qik_1_Y
 Could not find nucleotides of chain Y in annotation 6qik.json. Either there is a problem with 6qik mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
@@ -1540,8 +1546,11 @@ Could not find nucleotides of chain NC in annotation 6sv4.json. Either there is
 6i7o_1_NB
 Could not find nucleotides of chain NB in annotation 6i7o.json. Either there is a problem with 6i7o mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
-5y88_1_X
-Could not find nucleotides of chain X in annotation 5y88.json. Either there is a problem with 5y88 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+6swa_1_Q
+Could not find nucleotides of chain Q in annotation 6swa.json. Either there is a problem with 6swa mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
+6swa_1_R
+Could not find nucleotides of chain R in annotation 6swa.json. Either there is a problem with 6swa mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
 3j6x_1_IR
 Could not find nucleotides of chain IR in annotation 3j6x.json. Either there is a problem with 3j6x mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
@@ -2236,9 +2245,6 @@ DSSR warning 2r1g.json: no nucleotides found. Ignoring 2r1g_1_B.
 4ht9_1_E
 Sequence is too short. (< 5 resolved nts)
 
-1cvj_1_M
-Could not download and/or find annotations for 1cvj_1_M.
-
 6z1p_1_AB
 Could not find nucleotides of chain AB in annotation 6z1p.json. Either there is a problem with 6z1p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
@@ -2338,6 +2344,9 @@ Could not find nucleotides of chain N in annotation 6sv4.json. Either there is a
 6i7o_1_N
 Could not find nucleotides of chain N in annotation 6i7o.json. Either there is a problem with 6i7o mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
+6swa_1_S
+Could not find nucleotides of chain S in annotation 6swa.json. Either there is a problem with 6swa mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
 5k8h_1_A
 Sequence is too short. (< 5 resolved nts)
 
@@ -2677,9 +2686,6 @@ DSSR warning 1zn1.json: no nucleotides found. Ignoring 1zn1_1_B.
 6z8k_1_X
 Sequence is too short. (< 5 resolved nts)
 
-1cvj_1_Q
-Could not download and/or find annotations for 1cvj_1_Q.
-
 4csf_1_U
 Could not find nucleotides of chain U in annotation 4csf.json. Either there is a problem with 4csf mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
@@ -2716,24 +2722,6 @@ Could not find nucleotides of chain O in annotation 4csf.json. Either there is a
 4csf_1_E
 Could not find nucleotides of chain E in annotation 4csf.json. Either there is a problem with 4csf mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
-1cvj_1_N
-Could not download and/or find annotations for 1cvj_1_N.
-
-1cvj_1_O
-Could not download and/or find annotations for 1cvj_1_O.
-
-1cvj_1_S
-Could not download and/or find annotations for 1cvj_1_S.
-
-1cvj_1_P
-Could not download and/or find annotations for 1cvj_1_P.
-
-1cvj_1_T
-Could not download and/or find annotations for 1cvj_1_T.
-
-1cvj_1_R
-Could not download and/or find annotations for 1cvj_1_R.
-
 6th6_1_AA
 Could not find nucleotides of chain AA in annotation 6th6.json. Either there is a problem with 6th6 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
@@ -2957,7 +2945,7 @@ Sequence is too short. (< 5 resolved nts)
 DSSR warning 2iy3.json: no nucleotides found. Ignoring 2iy3_1_B.
 
 1cwp_1_F
-Could not download and/or find annotations for 1cwp_1_F.
+Sequence is too short. (< 5 resolved nts)
 
 5z4j_1_B
 Sequence is too short. (< 5 resolved nts)
@@ -3271,6 +3259,12 @@ Could not find nucleotides of chain II in annotation 5lzs.json. Either there is
 6fqr_1_C
 Sequence is too short. (< 5 resolved nts)
 
+2atw_1_B
+
+
+2atw_1_D
+
+
 6ha1_1_X
 Could not find nucleotides of chain X in annotation 6ha1.json. Either there is a problem with 6ha1 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
@@ -3523,6 +3517,9 @@ Sequence is too short. (< 5 resolved nts)
 4v5z_1_BC
 DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BC.
 
+5y88_1_X
+Could not find nucleotides of chain X in annotation 5y88.json. Either there is a problem with 5y88 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
 4v5z_1_BB
 DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BB.
 
@@ -3572,7 +3569,7 @@ Could not find nucleotides of chain A in annotation 3j0q.json. Either there is a
 Could not find nucleotides of chain A in annotation 3j0p.json. Either there is a problem with 3j0p mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
 1cwp_1_D
-Could not download and/or find annotations for 1cwp_1_D.
+Sequence is too short. (< 5 resolved nts)
 
 4v5z_1_BJ
 DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BJ.
@@ -3604,6 +3601,9 @@ Sequence is too short. (< 5 resolved nts)
 6ppn_1_I
 Sequence is too short. (< 5 resolved nts)
 
+6ys3_1_V
+Could not find nucleotides of chain V in annotation 6ys3.json. Either there is a problem with 6ys3 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
 6qdw_1_V
 Could not find nucleotides of chain V in annotation 6qdw.json. Either there is a problem with 6qdw mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
@@ -3715,6 +3715,9 @@ Could not find nucleotides of chain BB in annotation 5mrf.json. Either there is
 6gz4_1_BW
 Could not find nucleotides of chain BW in annotation 6gz4.json. Either there is a problem with 6gz4 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
+4v5z_1_BN
+DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BN.
+
 3j46_1_P
 Could not find nucleotides of chain P in annotation 3j46.json. Either there is a problem with 3j46 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
@@ -4063,6 +4066,18 @@ Could not find nucleotides of chain V in annotation 6v3a.json. Either there is a
 6v39_1_V
 Could not find nucleotides of chain V in annotation 6v39.json. Either there is a problem with 6v39 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
 
+2az0_1_C
+
+
+2az0_1_D
+
+
+2az2_1_C
+
+
+2az2_1_D
+Could not find nucleotides of chain D in annotation 2az2.json. Either there is a problem with 2az2 mmCIF download, or the bases are not resolved in the structure. Delete it and retry.
+
 5a0v_1_F
 Sequence is too short. (< 5 resolved nts)
 
@@ -4117,9 +4132,6 @@ DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BV.
 4v5z_1_BO
 DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BO.
 
-4v5z_1_BN
-DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BN.
-
 4v5z_1_BQ
 DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BQ.
 
@@ -4714,6 +4726,12 @@ Sequence is too short. (< 5 resolved nts)
 2a1r_1_C
 Sequence is too short. (< 5 resolved nts)
 
+6m6v_1_F
+Sequence is too short. (< 5 resolved nts)
+
+6m6v_1_E
+Sequence is too short. (< 5 resolved nts)
+
 2a1r_1_D
 Sequence is too short. (< 5 resolved nts)
 
@@ -4729,6 +4747,9 @@ Sequence is too short. (< 5 resolved nts)
 6vm6_1_K
 Sequence is too short. (< 5 resolved nts)
 
+6m6v_1_G
+Sequence is too short. (< 5 resolved nts)
+
 6hyu_1_D
 Sequence is too short. (< 5 resolved nts)
 

@@ -4,17 +4,19 @@ cd /home/lbecquey/Projects/RNANet
 rm -rf latest_run.log errors.txt
 
 # Run RNANet
-bash -c 'time ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -r 20.0 -s --archive' &> latest_run.log
+bash -c 'time ./RNAnet.py --3d-folder /home/lbecquey/Data/RNA/3D/ --seq-folder /home/lbecquey/Data/RNA/sequences/ -r 20.0 --extract -s --archive' > latest_run.log 2>&1
+echo 'Compressing RNANet.db.gz...' >> latest_run.log
 touch results/RNANet.db                                         # update last modification date
 gzip -k /home/lbecquey/Projects/RNANet/results/RNANet.db        # compress it
 rm -f results/RNANet.db-wal results/RNANet.db-shm               # SQLite temporary files
 
 # Save the latest results
-export DATE=`printf '%(%Y%m%d)T'`
+export DATE=`date +%Y%m%d`
+echo "Creating new release in ./archive/ folder ($DATE)..." >> latest_run.log
 cp /home/lbecquey/Projects/RNANet/results/summary.csv /home/lbecquey/Projects/RNANet/archive/summary_latest.csv
-cp /home/lbecquey/Projects/RNANet/results/summary.csv /home/lbecquey/Projects/RNANet/archive/summary_$DATE.csv
+cp /home/lbecquey/Projects/RNANet/results/summary.csv "/home/lbecquey/Projects/RNANet/archive/summary_$DATE.csv"
 cp /home/lbecquey/Projects/RNANet/results/families.csv /home/lbecquey/Projects/RNANet/archive/families_latest.csv
-cp /home/lbecquey/Projects/RNANet/results/families.csv /home/lbecquey/Projects/RNANet/archive/families_$DATE.csv
+cp /home/lbecquey/Projects/RNANet/results/families.csv "/home/lbecquey/Projects/RNANet/archive/families_$DATE.csv"
 cp /home/lbecquey/Projects/RNANet/results/frequencies.csv /home/lbecquey/Projects/RNANet/archive/frequencies_latest.csv
 cp /home/lbecquey/Projects/RNANet/results/pair_types.csv /home/lbecquey/Projects/RNANet/archive/pair_types_latest.csv
 mv /home/lbecquey/Projects/RNANet/results/RNANet.db.gz /home/lbecquey/Projects/RNANet/archive/