Job ID = 5720307 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,839,740 reads read : 25,839,740 reads written : 25,839,740 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: 00:06:10 25839740 reads; of these: 25839740 (100.00%) were unpaired; of these: 1338055 (5.18%) aligned 0 times 18060843 (69.90%) aligned exactly 1 time 6440842 (24.93%) aligned >1 times 94.82% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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 12 files... [bam_rmdupse_core] 4108485 / 24501685 = 0.1677 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 23:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.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 23:25:54: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:25:54: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:26:00: 1000000 INFO @ Wed, 15 Apr 2020 23:26:05: 2000000 INFO @ Wed, 15 Apr 2020 23:26:10: 3000000 INFO @ Wed, 15 Apr 2020 23:26:15: 4000000 INFO @ Wed, 15 Apr 2020 23:26:20: 5000000 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 23:26:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.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 23:26:24: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:26:24: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:26:25: 6000000 INFO @ Wed, 15 Apr 2020 23:26:29: 1000000 INFO @ Wed, 15 Apr 2020 23:26:30: 7000000 INFO @ Wed, 15 Apr 2020 23:26:34: 2000000 INFO @ Wed, 15 Apr 2020 23:26:35: 8000000 INFO @ Wed, 15 Apr 2020 23:26:39: 3000000 INFO @ Wed, 15 Apr 2020 23:26:39: 9000000 INFO @ Wed, 15 Apr 2020 23:26:43: 4000000 INFO @ Wed, 15 Apr 2020 23:26:44: 10000000 INFO @ Wed, 15 Apr 2020 23:26:48: 5000000 INFO @ Wed, 15 Apr 2020 23:26:49: 11000000 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 23:26:53: 6000000 INFO @ Wed, 15 Apr 2020 23:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.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 23:26:54: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:26:54: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:26:54: 12000000 INFO @ Wed, 15 Apr 2020 23:26:58: 7000000 INFO @ Wed, 15 Apr 2020 23:26:59: 13000000 INFO @ Wed, 15 Apr 2020 23:26:59: 1000000 INFO @ Wed, 15 Apr 2020 23:27:03: 8000000 INFO @ Wed, 15 Apr 2020 23:27:04: 14000000 INFO @ Wed, 15 Apr 2020 23:27:05: 2000000 INFO @ Wed, 15 Apr 2020 23:27:08: 9000000 INFO @ Wed, 15 Apr 2020 23:27:09: 15000000 INFO @ Wed, 15 Apr 2020 23:27:11: 3000000 INFO @ Wed, 15 Apr 2020 23:27:13: 10000000 INFO @ Wed, 15 Apr 2020 23:27:14: 16000000 INFO @ Wed, 15 Apr 2020 23:27:16: 4000000 INFO @ Wed, 15 Apr 2020 23:27:18: 11000000 INFO @ Wed, 15 Apr 2020 23:27:19: 17000000 INFO @ Wed, 15 Apr 2020 23:27:21: 5000000 INFO @ Wed, 15 Apr 2020 23:27:23: 12000000 INFO @ Wed, 15 Apr 2020 23:27:23: 18000000 INFO @ Wed, 15 Apr 2020 23:27:27: 6000000 INFO @ Wed, 15 Apr 2020 23:27:28: 13000000 INFO @ Wed, 15 Apr 2020 23:27:28: 19000000 INFO @ Wed, 15 Apr 2020 23:27:32: 7000000 INFO @ Wed, 15 Apr 2020 23:27:33: 14000000 INFO @ Wed, 15 Apr 2020 23:27:34: 20000000 INFO @ Wed, 15 Apr 2020 23:27:36: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:27:36: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:27:36: #1 total tags in treatment: 20393200 INFO @ Wed, 15 Apr 2020 23:27:36: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:27:36: #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 23:27:36: #1 tags after filtering in treatment: 20393200 INFO @ Wed, 15 Apr 2020 23:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:27:36: #1 finished! INFO @ Wed, 15 Apr 2020 23:27:36: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:27:37: 8000000 INFO @ Wed, 15 Apr 2020 23:27:37: 15000000 INFO @ Wed, 15 Apr 2020 23:27:37: #2 number of paired peaks: 380 WARNING @ Wed, 15 Apr 2020 23:27:37: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Wed, 15 Apr 2020 23:27:37: start model_add_line... INFO @ Wed, 15 Apr 2020 23:27:38: start X-correlation... INFO @ Wed, 15 Apr 2020 23:27:38: end of X-cor INFO @ Wed, 15 Apr 2020 23:27:38: #2 finished! INFO @ Wed, 15 Apr 2020 23:27:38: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 23:27:38: #2 alternative fragment length(s) may be 1,22 bps INFO @ Wed, 15 Apr 2020 23:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.05_model.r WARNING @ Wed, 15 Apr 2020 23:27:38: #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 23:27:38: #2 You may need to consider one of the other alternative d(s): 1,22 WARNING @ Wed, 15 Apr 2020 23:27:38: #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 23:27:38: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:27:42: 16000000 INFO @ Wed, 15 Apr 2020 23:27:43: 9000000 INFO @ Wed, 15 Apr 2020 23:27:47: 17000000 INFO @ Wed, 15 Apr 2020 23:27:48: 10000000 INFO @ Wed, 15 Apr 2020 23:27:52: 18000000 INFO @ Wed, 15 Apr 2020 23:27:53: 11000000 INFO @ Wed, 15 Apr 2020 23:27:57: 19000000 INFO @ Wed, 15 Apr 2020 23:27:58: 12000000 INFO @ Wed, 15 Apr 2020 23:28:02: 20000000 INFO @ Wed, 15 Apr 2020 23:28:03: 13000000 INFO @ Wed, 15 Apr 2020 23:28:04: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:28:04: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:28:04: #1 total tags in treatment: 20393200 INFO @ Wed, 15 Apr 2020 23:28:04: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:28:04: #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 23:28:04: #1 tags after filtering in treatment: 20393200 INFO @ Wed, 15 Apr 2020 23:28:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:28:04: #1 finished! INFO @ Wed, 15 Apr 2020 23:28:04: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:28:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:28:06: #2 number of paired peaks: 380 WARNING @ Wed, 15 Apr 2020 23:28:06: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Wed, 15 Apr 2020 23:28:06: start model_add_line... INFO @ Wed, 15 Apr 2020 23:28:06: start X-correlation... INFO @ Wed, 15 Apr 2020 23:28:06: end of X-cor INFO @ Wed, 15 Apr 2020 23:28:06: #2 finished! INFO @ Wed, 15 Apr 2020 23:28:06: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 23:28:06: #2 alternative fragment length(s) may be 1,22 bps INFO @ Wed, 15 Apr 2020 23:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.10_model.r WARNING @ Wed, 15 Apr 2020 23:28:06: #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 23:28:06: #2 You may need to consider one of the other alternative d(s): 1,22 WARNING @ Wed, 15 Apr 2020 23:28:06: #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 23:28:06: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:28:08: 14000000 INFO @ Wed, 15 Apr 2020 23:28:10: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:28:13: 15000000 INFO @ Wed, 15 Apr 2020 23:28:18: 16000000 INFO @ Wed, 15 Apr 2020 23:28:23: 17000000 INFO @ Wed, 15 Apr 2020 23:28:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:28:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:28:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.05_summits.bed INFO @ Wed, 15 Apr 2020 23:28:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:28:27: 18000000 INFO @ Wed, 15 Apr 2020 23:28:33: 19000000 INFO @ Wed, 15 Apr 2020 23:28:38: 20000000 INFO @ Wed, 15 Apr 2020 23:28:39: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:28:40: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:28:40: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:28:40: #1 total tags in treatment: 20393200 INFO @ Wed, 15 Apr 2020 23:28:40: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:28:40: #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 23:28:40: #1 tags after filtering in treatment: 20393200 INFO @ Wed, 15 Apr 2020 23:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:28:40: #1 finished! INFO @ Wed, 15 Apr 2020 23:28:40: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:28:42: #2 number of paired peaks: 380 WARNING @ Wed, 15 Apr 2020 23:28:42: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Wed, 15 Apr 2020 23:28:42: start model_add_line... INFO @ Wed, 15 Apr 2020 23:28:42: start X-correlation... INFO @ Wed, 15 Apr 2020 23:28:42: end of X-cor INFO @ Wed, 15 Apr 2020 23:28:42: #2 finished! INFO @ Wed, 15 Apr 2020 23:28:42: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 23:28:42: #2 alternative fragment length(s) may be 1,22 bps INFO @ Wed, 15 Apr 2020 23:28:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.20_model.r WARNING @ Wed, 15 Apr 2020 23:28:42: #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 23:28:42: #2 You may need to consider one of the other alternative d(s): 1,22 WARNING @ Wed, 15 Apr 2020 23:28:42: #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 23:28:42: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:28:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.10_summits.bed INFO @ Wed, 15 Apr 2020 23:28:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:29:15: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627554/SRX7627554.20_summits.bed INFO @ Wed, 15 Apr 2020 23:29:30: 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。