Job ID = 2641131 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T12:32:37 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 11,228,624 reads read : 22,457,248 reads written : 22,457,248 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:04 11228624 reads; of these: 11228624 (100.00%) were paired; of these: 5968307 (53.15%) aligned concordantly 0 times 4613855 (41.09%) aligned concordantly exactly 1 time 646462 (5.76%) aligned concordantly >1 times ---- 5968307 pairs aligned concordantly 0 times; of these: 4444610 (74.47%) aligned discordantly 1 time ---- 1523697 pairs aligned 0 times concordantly or discordantly; of these: 3047394 mates make up the pairs; of these: 1516084 (49.75%) aligned 0 times 179895 (5.90%) aligned exactly 1 time 1351415 (44.35%) aligned >1 times 93.25% overall alignment rate Time searching: 00:16:04 Overall time: 00:16:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 541121 / 9703674 = 0.0558 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 24 Aug 2019 22:14:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:14:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:14:24: 1000000 INFO @ Sat, 24 Aug 2019 22:14:32: 2000000 INFO @ Sat, 24 Aug 2019 22:14:40: 3000000 INFO @ Sat, 24 Aug 2019 22:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 24 Aug 2019 22:14:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:14:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:14:48: 4000000 INFO @ Sat, 24 Aug 2019 22:14:53: 1000000 INFO @ Sat, 24 Aug 2019 22:14:57: 5000000 INFO @ Sat, 24 Aug 2019 22:15:02: 2000000 INFO @ Sat, 24 Aug 2019 22:15:05: 6000000 INFO @ Sat, 24 Aug 2019 22:15:10: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:15:14: 7000000 INFO @ Sat, 24 Aug 2019 22:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 24 Aug 2019 22:15:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:15:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:15:19: 4000000 INFO @ Sat, 24 Aug 2019 22:15:22: 8000000 INFO @ Sat, 24 Aug 2019 22:15:24: 1000000 INFO @ Sat, 24 Aug 2019 22:15:28: 5000000 INFO @ Sat, 24 Aug 2019 22:15:30: 9000000 INFO @ Sat, 24 Aug 2019 22:15:34: 2000000 INFO @ Sat, 24 Aug 2019 22:15:37: 6000000 INFO @ Sat, 24 Aug 2019 22:15:39: 10000000 INFO @ Sat, 24 Aug 2019 22:15:43: 3000000 INFO @ Sat, 24 Aug 2019 22:15:47: 7000000 INFO @ Sat, 24 Aug 2019 22:15:47: 11000000 INFO @ Sat, 24 Aug 2019 22:15:53: 4000000 INFO @ Sat, 24 Aug 2019 22:15:56: 12000000 INFO @ Sat, 24 Aug 2019 22:15:56: 8000000 INFO @ Sat, 24 Aug 2019 22:16:02: 5000000 INFO @ Sat, 24 Aug 2019 22:16:04: 13000000 INFO @ Sat, 24 Aug 2019 22:16:05: 9000000 INFO @ Sat, 24 Aug 2019 22:16:11: 6000000 INFO @ Sat, 24 Aug 2019 22:16:13: 14000000 INFO @ Sat, 24 Aug 2019 22:16:14: 10000000 INFO @ Sat, 24 Aug 2019 22:16:20: 7000000 INFO @ Sat, 24 Aug 2019 22:16:21: 15000000 INFO @ Sat, 24 Aug 2019 22:16:23: 11000000 INFO @ Sat, 24 Aug 2019 22:16:30: 8000000 INFO @ Sat, 24 Aug 2019 22:16:30: 16000000 INFO @ Sat, 24 Aug 2019 22:16:32: 12000000 INFO @ Sat, 24 Aug 2019 22:16:38: 17000000 INFO @ Sat, 24 Aug 2019 22:16:39: 9000000 INFO @ Sat, 24 Aug 2019 22:16:42: 13000000 INFO @ Sat, 24 Aug 2019 22:16:47: 18000000 INFO @ Sat, 24 Aug 2019 22:16:48: 10000000 INFO @ Sat, 24 Aug 2019 22:16:51: 14000000 INFO @ Sat, 24 Aug 2019 22:16:55: 19000000 INFO @ Sat, 24 Aug 2019 22:16:57: 11000000 INFO @ Sat, 24 Aug 2019 22:17:00: 15000000 INFO @ Sat, 24 Aug 2019 22:17:02: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:17:02: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:17:02: #1 total tags in treatment: 4954085 INFO @ Sat, 24 Aug 2019 22:17:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:17:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:17:02: #1 tags after filtering in treatment: 4028082 INFO @ Sat, 24 Aug 2019 22:17:02: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:17:02: #1 finished! INFO @ Sat, 24 Aug 2019 22:17:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:17:03: #2 number of paired peaks: 150 WARNING @ Sat, 24 Aug 2019 22:17:03: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 24 Aug 2019 22:17:03: start model_add_line... INFO @ Sat, 24 Aug 2019 22:17:03: start X-correlation... INFO @ Sat, 24 Aug 2019 22:17:03: end of X-cor INFO @ Sat, 24 Aug 2019 22:17:03: #2 finished! INFO @ Sat, 24 Aug 2019 22:17:03: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:17:03: #2 alternative fragment length(s) may be 0,36,53,98,118,140,153,175,220,263,286,309,328,361,366,374,399,408,422,442,461,467,495,518,531,553,572,587 bps INFO @ Sat, 24 Aug 2019 22:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.05_model.r WARNING @ Sat, 24 Aug 2019 22:17:03: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 22:17:03: #2 You may need to consider one of the other alternative d(s): 0,36,53,98,118,140,153,175,220,263,286,309,328,361,366,374,399,408,422,442,461,467,495,518,531,553,572,587 WARNING @ Sat, 24 Aug 2019 22:17:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 22:17:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:17:07: 12000000 INFO @ Sat, 24 Aug 2019 22:17:09: 16000000 INFO @ Sat, 24 Aug 2019 22:17:16: 13000000 INFO @ Sat, 24 Aug 2019 22:17:18: 17000000 INFO @ Sat, 24 Aug 2019 22:17:25: 14000000 INFO @ Sat, 24 Aug 2019 22:17:27: 18000000 INFO @ Sat, 24 Aug 2019 22:17:34: 15000000 INFO @ Sat, 24 Aug 2019 22:17:36: 19000000 INFO @ Sat, 24 Aug 2019 22:17:43: 16000000 INFO @ Sat, 24 Aug 2019 22:17:44: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:17:44: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:17:44: #1 total tags in treatment: 4954085 INFO @ Sat, 24 Aug 2019 22:17:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:17:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:17:44: #1 tags after filtering in treatment: 4028082 INFO @ Sat, 24 Aug 2019 22:17:44: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:17:44: #1 finished! INFO @ Sat, 24 Aug 2019 22:17:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:17:44: #2 number of paired peaks: 150 WARNING @ Sat, 24 Aug 2019 22:17:44: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 24 Aug 2019 22:17:44: start model_add_line... INFO @ Sat, 24 Aug 2019 22:17:44: start X-correlation... INFO @ Sat, 24 Aug 2019 22:17:44: end of X-cor INFO @ Sat, 24 Aug 2019 22:17:44: #2 finished! INFO @ Sat, 24 Aug 2019 22:17:44: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:17:44: #2 alternative fragment length(s) may be 0,36,53,98,118,140,153,175,220,263,286,309,328,361,366,374,399,408,422,442,461,467,495,518,531,553,572,587 bps INFO @ Sat, 24 Aug 2019 22:17:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.10_model.r WARNING @ Sat, 24 Aug 2019 22:17:44: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 22:17:44: #2 You may need to consider one of the other alternative d(s): 0,36,53,98,118,140,153,175,220,263,286,309,328,361,366,374,399,408,422,442,461,467,495,518,531,553,572,587 WARNING @ Sat, 24 Aug 2019 22:17:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 22:17:44: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:17:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:17:51: 17000000 INFO @ Sat, 24 Aug 2019 22:17:59: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:18:07: 19000000 INFO @ Sat, 24 Aug 2019 22:18:14: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:18:14: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:18:14: #1 total tags in treatment: 4954085 INFO @ Sat, 24 Aug 2019 22:18:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:18:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:18:14: #1 tags after filtering in treatment: 4028082 INFO @ Sat, 24 Aug 2019 22:18:14: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:18:14: #1 finished! INFO @ Sat, 24 Aug 2019 22:18:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:18:15: #2 number of paired peaks: 150 WARNING @ Sat, 24 Aug 2019 22:18:15: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Sat, 24 Aug 2019 22:18:15: start model_add_line... INFO @ Sat, 24 Aug 2019 22:18:15: start X-correlation... INFO @ Sat, 24 Aug 2019 22:18:15: end of X-cor INFO @ Sat, 24 Aug 2019 22:18:15: #2 finished! INFO @ Sat, 24 Aug 2019 22:18:15: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:18:15: #2 alternative fragment length(s) may be 0,36,53,98,118,140,153,175,220,263,286,309,328,361,366,374,399,408,422,442,461,467,495,518,531,553,572,587 bps INFO @ Sat, 24 Aug 2019 22:18:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546568/SRX5546568.20_model.r WARNING @ Sat, 24 Aug 2019 22:18:15: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 22:18:15: #2 You may need to consider one of the other alternative d(s): 0,36,53,98,118,140,153,175,220,263,286,309,328,361,366,374,399,408,422,442,461,467,495,518,531,553,572,587 WARNING @ Sat, 24 Aug 2019 22:18:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 22:18:15: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:18:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at099/job_scripts/2641131: line 336: 50693 Terminated MACS $i /var/spool/uge/at099/job_scripts/2641131: line 336: 50748 Terminated MACS $i /var/spool/uge/at099/job_scripts/2641131: line 336: 50786 Terminated MACS $i ls: cannot access SRX5546568.05.bed: No such file or directory mv: cannot stat ‘SRX5546568.05.bed’: No such file or directory mv: cannot stat ‘SRX5546568.05.bb’: No such file or directory ls: cannot access SRX5546568.10.bed: No such file or directory mv: cannot stat ‘SRX5546568.10.bed’: No such file or directory mv: cannot stat ‘SRX5546568.10.bb’: No such file or directory ls: cannot access SRX5546568.20.bed: No such file or directory mv: cannot stat ‘SRX5546568.20.bed’: No such file or directory mv: cannot stat ‘SRX5546568.20.bb’: No such file or directory