Job ID = 5720207 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,437,324 reads read : 74,874,648 reads written : 37,437,324 reads 0-length : 37,437,324 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: 00:07:16 37437324 reads; of these: 37437324 (100.00%) were unpaired; of these: 3098741 (8.28%) aligned 0 times 28630811 (76.48%) aligned exactly 1 time 5707772 (15.25%) aligned >1 times 91.72% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 6995159 / 34338583 = 0.2037 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 21:57:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.bam'] # control file = None # effective genome size = 9.00e+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 @ Wed, 15 Apr 2020 21:57:43: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:57:43: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:57:47: 1000000 INFO @ Wed, 15 Apr 2020 21:57:52: 2000000 INFO @ Wed, 15 Apr 2020 21:57:56: 3000000 INFO @ Wed, 15 Apr 2020 21:58:01: 4000000 INFO @ Wed, 15 Apr 2020 21:58:05: 5000000 INFO @ Wed, 15 Apr 2020 21:58:10: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 21:58:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.bam'] # control file = None # effective genome size = 9.00e+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 @ Wed, 15 Apr 2020 21:58:12: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:58:12: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:58:14: 7000000 INFO @ Wed, 15 Apr 2020 21:58:18: 1000000 INFO @ Wed, 15 Apr 2020 21:58:19: 8000000 INFO @ Wed, 15 Apr 2020 21:58:23: 2000000 INFO @ Wed, 15 Apr 2020 21:58:24: 9000000 INFO @ Wed, 15 Apr 2020 21:58:28: 3000000 INFO @ Wed, 15 Apr 2020 21:58:28: 10000000 INFO @ Wed, 15 Apr 2020 21:58:33: 11000000 INFO @ Wed, 15 Apr 2020 21:58:34: 4000000 INFO @ Wed, 15 Apr 2020 21:58:38: 12000000 INFO @ Wed, 15 Apr 2020 21:58:39: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 21:58:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.bam'] # control file = None # effective genome size = 9.00e+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 @ Wed, 15 Apr 2020 21:58:42: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:58:42: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:58:43: 13000000 INFO @ Wed, 15 Apr 2020 21:58:44: 6000000 INFO @ Wed, 15 Apr 2020 21:58:47: 1000000 INFO @ Wed, 15 Apr 2020 21:58:47: 14000000 INFO @ Wed, 15 Apr 2020 21:58:50: 7000000 INFO @ Wed, 15 Apr 2020 21:58:52: 2000000 INFO @ Wed, 15 Apr 2020 21:58:52: 15000000 INFO @ Wed, 15 Apr 2020 21:58:55: 8000000 INFO @ Wed, 15 Apr 2020 21:58:56: 3000000 INFO @ Wed, 15 Apr 2020 21:58:57: 16000000 INFO @ Wed, 15 Apr 2020 21:59:00: 9000000 INFO @ Wed, 15 Apr 2020 21:59:01: 4000000 INFO @ Wed, 15 Apr 2020 21:59:02: 17000000 INFO @ Wed, 15 Apr 2020 21:59:06: 10000000 INFO @ Wed, 15 Apr 2020 21:59:06: 5000000 INFO @ Wed, 15 Apr 2020 21:59:06: 18000000 INFO @ Wed, 15 Apr 2020 21:59:11: 6000000 INFO @ Wed, 15 Apr 2020 21:59:11: 11000000 INFO @ Wed, 15 Apr 2020 21:59:11: 19000000 INFO @ Wed, 15 Apr 2020 21:59:16: 7000000 INFO @ Wed, 15 Apr 2020 21:59:16: 20000000 INFO @ Wed, 15 Apr 2020 21:59:16: 12000000 INFO @ Wed, 15 Apr 2020 21:59:20: 8000000 INFO @ Wed, 15 Apr 2020 21:59:21: 21000000 INFO @ Wed, 15 Apr 2020 21:59:22: 13000000 INFO @ Wed, 15 Apr 2020 21:59:25: 22000000 INFO @ Wed, 15 Apr 2020 21:59:25: 9000000 INFO @ Wed, 15 Apr 2020 21:59:27: 14000000 INFO @ Wed, 15 Apr 2020 21:59:30: 10000000 INFO @ Wed, 15 Apr 2020 21:59:30: 23000000 INFO @ Wed, 15 Apr 2020 21:59:32: 15000000 INFO @ Wed, 15 Apr 2020 21:59:35: 11000000 INFO @ Wed, 15 Apr 2020 21:59:35: 24000000 INFO @ Wed, 15 Apr 2020 21:59:38: 16000000 INFO @ Wed, 15 Apr 2020 21:59:40: 25000000 INFO @ Wed, 15 Apr 2020 21:59:40: 12000000 INFO @ Wed, 15 Apr 2020 21:59:43: 17000000 INFO @ Wed, 15 Apr 2020 21:59:44: 26000000 INFO @ Wed, 15 Apr 2020 21:59:44: 13000000 INFO @ Wed, 15 Apr 2020 21:59:48: 18000000 INFO @ Wed, 15 Apr 2020 21:59:49: 27000000 INFO @ Wed, 15 Apr 2020 21:59:49: 14000000 INFO @ Wed, 15 Apr 2020 21:59:51: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 21:59:51: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 21:59:51: #1 total tags in treatment: 27343424 INFO @ Wed, 15 Apr 2020 21:59:51: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 21:59:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 21:59:51: #1 tags after filtering in treatment: 27343424 INFO @ Wed, 15 Apr 2020 21:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 21:59:51: #1 finished! INFO @ Wed, 15 Apr 2020 21:59:51: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 21:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 21:59:53: #2 number of paired peaks: 101 WARNING @ Wed, 15 Apr 2020 21:59:53: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Wed, 15 Apr 2020 21:59:53: start model_add_line... INFO @ Wed, 15 Apr 2020 21:59:53: start X-correlation... INFO @ Wed, 15 Apr 2020 21:59:53: end of X-cor INFO @ Wed, 15 Apr 2020 21:59:53: #2 finished! INFO @ Wed, 15 Apr 2020 21:59:53: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 21:59:53: #2 alternative fragment length(s) may be 1,41,590 bps INFO @ Wed, 15 Apr 2020 21:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.05_model.r WARNING @ Wed, 15 Apr 2020 21:59:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 21:59:53: #2 You may need to consider one of the other alternative d(s): 1,41,590 WARNING @ Wed, 15 Apr 2020 21:59:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 21:59:53: #3 Call peaks... INFO @ Wed, 15 Apr 2020 21:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 21:59:54: 19000000 INFO @ Wed, 15 Apr 2020 21:59:54: 15000000 INFO @ Wed, 15 Apr 2020 21:59:59: 16000000 INFO @ Wed, 15 Apr 2020 21:59:59: 20000000 INFO @ Wed, 15 Apr 2020 22:00:03: 17000000 INFO @ Wed, 15 Apr 2020 22:00:04: 21000000 INFO @ Wed, 15 Apr 2020 22:00:08: 18000000 INFO @ Wed, 15 Apr 2020 22:00:10: 22000000 INFO @ Wed, 15 Apr 2020 22:00:13: 19000000 INFO @ Wed, 15 Apr 2020 22:00:15: 23000000 INFO @ Wed, 15 Apr 2020 22:00:18: 20000000 INFO @ Wed, 15 Apr 2020 22:00:20: 24000000 INFO @ Wed, 15 Apr 2020 22:00:22: 21000000 INFO @ Wed, 15 Apr 2020 22:00:26: 25000000 INFO @ Wed, 15 Apr 2020 22:00:27: 22000000 INFO @ Wed, 15 Apr 2020 22:00:31: 26000000 INFO @ Wed, 15 Apr 2020 22:00:31: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:00:32: 23000000 INFO @ Wed, 15 Apr 2020 22:00:36: 27000000 INFO @ Wed, 15 Apr 2020 22:00:37: 24000000 INFO @ Wed, 15 Apr 2020 22:00:38: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:00:38: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:00:38: #1 total tags in treatment: 27343424 INFO @ Wed, 15 Apr 2020 22:00:38: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:00:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:00:39: #1 tags after filtering in treatment: 27343424 INFO @ Wed, 15 Apr 2020 22:00:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:00:39: #1 finished! INFO @ Wed, 15 Apr 2020 22:00:39: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:00:40: #2 number of paired peaks: 101 WARNING @ Wed, 15 Apr 2020 22:00:40: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Wed, 15 Apr 2020 22:00:40: start model_add_line... INFO @ Wed, 15 Apr 2020 22:00:41: start X-correlation... INFO @ Wed, 15 Apr 2020 22:00:41: end of X-cor INFO @ Wed, 15 Apr 2020 22:00:41: #2 finished! INFO @ Wed, 15 Apr 2020 22:00:41: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:00:41: #2 alternative fragment length(s) may be 1,41,590 bps INFO @ Wed, 15 Apr 2020 22:00:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.10_model.r WARNING @ Wed, 15 Apr 2020 22:00:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:00:41: #2 You may need to consider one of the other alternative d(s): 1,41,590 WARNING @ Wed, 15 Apr 2020 22:00:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:00:41: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:00:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:00:42: 25000000 INFO @ Wed, 15 Apr 2020 22:00:46: 26000000 INFO @ Wed, 15 Apr 2020 22:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.05_summits.bed INFO @ Wed, 15 Apr 2020 22:00:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:00:51: 27000000 INFO @ Wed, 15 Apr 2020 22:00:53: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:00:53: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:00:53: #1 total tags in treatment: 27343424 INFO @ Wed, 15 Apr 2020 22:00:53: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:00:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:00:53: #1 tags after filtering in treatment: 27343424 INFO @ Wed, 15 Apr 2020 22:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:00:53: #1 finished! INFO @ Wed, 15 Apr 2020 22:00:53: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:00:55: #2 number of paired peaks: 101 WARNING @ Wed, 15 Apr 2020 22:00:55: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Wed, 15 Apr 2020 22:00:55: start model_add_line... INFO @ Wed, 15 Apr 2020 22:00:55: start X-correlation... INFO @ Wed, 15 Apr 2020 22:00:55: end of X-cor INFO @ Wed, 15 Apr 2020 22:00:55: #2 finished! INFO @ Wed, 15 Apr 2020 22:00:55: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:00:55: #2 alternative fragment length(s) may be 1,41,590 bps INFO @ Wed, 15 Apr 2020 22:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.20_model.r WARNING @ Wed, 15 Apr 2020 22:00:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:00:55: #2 You may need to consider one of the other alternative d(s): 1,41,590 WARNING @ Wed, 15 Apr 2020 22:00:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:00:55: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:01:18: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:01:33: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:01:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.10_summits.bed INFO @ Wed, 15 Apr 2020 22:01:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619575/SRX6619575.20_summits.bed INFO @ Wed, 15 Apr 2020 22:01:50: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。