Job ID = 6367623 SRX = SRX3583335 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:20 prefetch.2.10.7: 1) Downloading 'SRR6493991'... 2020-06-15T23:33:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:08 prefetch.2.10.7: 1) 'SRR6493991' was downloaded successfully 2020-06-15T23:39:08 prefetch.2.10.7: 'SRR6493991' has 0 unresolved dependencies Read 36795442 spots for SRR6493991/SRR6493991.sra Written 36795442 spots for SRR6493991/SRR6493991.sra 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: 00:11:05 36795442 reads; of these: 36795442 (100.00%) were unpaired; of these: 6314445 (17.16%) aligned 0 times 26168489 (71.12%) aligned exactly 1 time 4312508 (11.72%) aligned >1 times 82.84% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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] 7761985 / 30480997 = 0.2546 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 @ Tue, 16 Jun 2020 08:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.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 @ Tue, 16 Jun 2020 08:59:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:39: 1000000 INFO @ Tue, 16 Jun 2020 08:59:45: 2000000 INFO @ Tue, 16 Jun 2020 08:59:52: 3000000 INFO @ Tue, 16 Jun 2020 08:59:58: 4000000 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 @ Tue, 16 Jun 2020 09:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.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 @ Tue, 16 Jun 2020 09:00:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:05: 5000000 INFO @ Tue, 16 Jun 2020 09:00:09: 1000000 INFO @ Tue, 16 Jun 2020 09:00:12: 6000000 INFO @ Tue, 16 Jun 2020 09:00:17: 2000000 INFO @ Tue, 16 Jun 2020 09:00:19: 7000000 INFO @ Tue, 16 Jun 2020 09:00:24: 3000000 INFO @ Tue, 16 Jun 2020 09:00:27: 8000000 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 @ Tue, 16 Jun 2020 09:00:31: 4000000 INFO @ Tue, 16 Jun 2020 09:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.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 @ Tue, 16 Jun 2020 09:00:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:34: 9000000 INFO @ Tue, 16 Jun 2020 09:00:39: 5000000 INFO @ Tue, 16 Jun 2020 09:00:40: 1000000 INFO @ Tue, 16 Jun 2020 09:00:41: 10000000 INFO @ Tue, 16 Jun 2020 09:00:46: 6000000 INFO @ Tue, 16 Jun 2020 09:00:47: 2000000 INFO @ Tue, 16 Jun 2020 09:00:49: 11000000 INFO @ Tue, 16 Jun 2020 09:00:53: 7000000 INFO @ Tue, 16 Jun 2020 09:00:55: 3000000 INFO @ Tue, 16 Jun 2020 09:00:56: 12000000 INFO @ Tue, 16 Jun 2020 09:01:00: 8000000 INFO @ Tue, 16 Jun 2020 09:01:02: 4000000 INFO @ Tue, 16 Jun 2020 09:01:03: 13000000 INFO @ Tue, 16 Jun 2020 09:01:08: 9000000 INFO @ Tue, 16 Jun 2020 09:01:09: 5000000 INFO @ Tue, 16 Jun 2020 09:01:10: 14000000 INFO @ Tue, 16 Jun 2020 09:01:15: 10000000 INFO @ Tue, 16 Jun 2020 09:01:17: 6000000 INFO @ Tue, 16 Jun 2020 09:01:18: 15000000 INFO @ Tue, 16 Jun 2020 09:01:22: 11000000 INFO @ Tue, 16 Jun 2020 09:01:24: 7000000 INFO @ Tue, 16 Jun 2020 09:01:25: 16000000 INFO @ Tue, 16 Jun 2020 09:01:29: 12000000 INFO @ Tue, 16 Jun 2020 09:01:31: 8000000 INFO @ Tue, 16 Jun 2020 09:01:32: 17000000 INFO @ Tue, 16 Jun 2020 09:01:37: 13000000 INFO @ Tue, 16 Jun 2020 09:01:38: 9000000 INFO @ Tue, 16 Jun 2020 09:01:40: 18000000 INFO @ Tue, 16 Jun 2020 09:01:44: 14000000 INFO @ Tue, 16 Jun 2020 09:01:46: 10000000 INFO @ Tue, 16 Jun 2020 09:01:47: 19000000 INFO @ Tue, 16 Jun 2020 09:01:51: 15000000 INFO @ Tue, 16 Jun 2020 09:01:53: 11000000 INFO @ Tue, 16 Jun 2020 09:01:55: 20000000 INFO @ Tue, 16 Jun 2020 09:01:59: 16000000 INFO @ Tue, 16 Jun 2020 09:02:00: 12000000 INFO @ Tue, 16 Jun 2020 09:02:02: 21000000 INFO @ Tue, 16 Jun 2020 09:02:06: 17000000 INFO @ Tue, 16 Jun 2020 09:02:08: 13000000 INFO @ Tue, 16 Jun 2020 09:02:10: 22000000 INFO @ Tue, 16 Jun 2020 09:02:14: 18000000 INFO @ Tue, 16 Jun 2020 09:02:15: 14000000 INFO @ Tue, 16 Jun 2020 09:02:15: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:02:15: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:02:15: #1 total tags in treatment: 22719012 INFO @ Tue, 16 Jun 2020 09:02:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:02:16: #1 tags after filtering in treatment: 22719012 INFO @ Tue, 16 Jun 2020 09:02:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:16: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:17: #2 number of paired peaks: 128 WARNING @ Tue, 16 Jun 2020 09:02:17: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:18: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:02:18: #2 alternative fragment length(s) may be 2,21,59,567 bps INFO @ Tue, 16 Jun 2020 09:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.05_model.r WARNING @ Tue, 16 Jun 2020 09:02:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:18: #2 You may need to consider one of the other alternative d(s): 2,21,59,567 WARNING @ Tue, 16 Jun 2020 09:02:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:02:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:21: 19000000 INFO @ Tue, 16 Jun 2020 09:02:23: 15000000 INFO @ Tue, 16 Jun 2020 09:02:29: 20000000 INFO @ Tue, 16 Jun 2020 09:02:30: 16000000 INFO @ Tue, 16 Jun 2020 09:02:36: 21000000 INFO @ Tue, 16 Jun 2020 09:02:38: 17000000 INFO @ Tue, 16 Jun 2020 09:02:44: 22000000 INFO @ Tue, 16 Jun 2020 09:02:45: 18000000 INFO @ Tue, 16 Jun 2020 09:02:49: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:02:49: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:02:49: #1 total tags in treatment: 22719012 INFO @ Tue, 16 Jun 2020 09:02:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:02:49: #1 tags after filtering in treatment: 22719012 INFO @ Tue, 16 Jun 2020 09:02:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:51: #2 number of paired peaks: 128 WARNING @ Tue, 16 Jun 2020 09:02:51: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:51: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:02:51: #2 alternative fragment length(s) may be 2,21,59,567 bps INFO @ Tue, 16 Jun 2020 09:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.10_model.r WARNING @ Tue, 16 Jun 2020 09:02:51: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:51: #2 You may need to consider one of the other alternative d(s): 2,21,59,567 WARNING @ Tue, 16 Jun 2020 09:02:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:02:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:53: 19000000 INFO @ Tue, 16 Jun 2020 09:02:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:59: 20000000 INFO @ Tue, 16 Jun 2020 09:03:06: 21000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.05_summits.bed INFO @ Tue, 16 Jun 2020 09:03:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:12: 22000000 INFO @ Tue, 16 Jun 2020 09:03:17: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:03:17: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:03:17: #1 total tags in treatment: 22719012 INFO @ Tue, 16 Jun 2020 09:03:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:03:17: #1 tags after filtering in treatment: 22719012 INFO @ Tue, 16 Jun 2020 09:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:19: #2 number of paired peaks: 128 WARNING @ Tue, 16 Jun 2020 09:03:19: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:19: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:03:19: #2 alternative fragment length(s) may be 2,21,59,567 bps INFO @ Tue, 16 Jun 2020 09:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.20_model.r WARNING @ Tue, 16 Jun 2020 09:03:19: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:19: #2 You may need to consider one of the other alternative d(s): 2,21,59,567 WARNING @ Tue, 16 Jun 2020 09:03:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:03:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583335/SRX3583335.20_summits.bed INFO @ Tue, 16 Jun 2020 09:04:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling