Job ID = 6368118 SRX = SRX466581 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:54:22 prefetch.2.10.7: 1) Downloading 'SRR1163647'... 2020-06-15T23:54:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:56:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:56:15 prefetch.2.10.7: 1) 'SRR1163647' was downloaded successfully Read 18388946 spots for SRR1163647/SRR1163647.sra Written 18388946 spots for SRR1163647/SRR1163647.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: 00:03:50 18388946 reads; of these: 18388946 (100.00%) were unpaired; of these: 4337264 (23.59%) aligned 0 times 11667965 (63.45%) aligned exactly 1 time 2383717 (12.96%) aligned >1 times 76.41% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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 8 files... [bam_rmdupse_core] 1118059 / 14051682 = 0.0796 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 09:05:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.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 09:05:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:12: 1000000 INFO @ Tue, 16 Jun 2020 09:05:17: 2000000 INFO @ Tue, 16 Jun 2020 09:05:22: 3000000 INFO @ Tue, 16 Jun 2020 09:05:28: 4000000 INFO @ Tue, 16 Jun 2020 09:05:33: 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 @ Tue, 16 Jun 2020 09:05:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.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 09:05:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:38: 6000000 INFO @ Tue, 16 Jun 2020 09:05:43: 1000000 INFO @ Tue, 16 Jun 2020 09:05:44: 7000000 INFO @ Tue, 16 Jun 2020 09:05:48: 2000000 INFO @ Tue, 16 Jun 2020 09:05:50: 8000000 INFO @ Tue, 16 Jun 2020 09:05:54: 3000000 INFO @ Tue, 16 Jun 2020 09:05:55: 9000000 INFO @ Tue, 16 Jun 2020 09:05:59: 4000000 INFO @ Tue, 16 Jun 2020 09:06:01: 10000000 INFO @ Tue, 16 Jun 2020 09:06:05: 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 @ Tue, 16 Jun 2020 09:06:07: 11000000 INFO @ Tue, 16 Jun 2020 09:06:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.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 09:06:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:11: 6000000 INFO @ Tue, 16 Jun 2020 09:06:13: 12000000 INFO @ Tue, 16 Jun 2020 09:06:14: 1000000 INFO @ Tue, 16 Jun 2020 09:06:17: 7000000 INFO @ Tue, 16 Jun 2020 09:06:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:06:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:06:18: #1 total tags in treatment: 12933623 INFO @ Tue, 16 Jun 2020 09:06:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:18: #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 09:06:19: #1 tags after filtering in treatment: 12933623 INFO @ Tue, 16 Jun 2020 09:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:19: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:06:19: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:06:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:20: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:06:20: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 09:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.05_model.r WARNING @ Tue, 16 Jun 2020 09:06:20: #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 09:06:20: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 09:06:20: #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 09:06:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:06:20: 2000000 INFO @ Tue, 16 Jun 2020 09:06:23: 8000000 INFO @ Tue, 16 Jun 2020 09:06:27: 3000000 INFO @ Tue, 16 Jun 2020 09:06:29: 9000000 INFO @ Tue, 16 Jun 2020 09:06:33: 4000000 INFO @ Tue, 16 Jun 2020 09:06:35: 10000000 INFO @ Tue, 16 Jun 2020 09:06:40: 5000000 INFO @ Tue, 16 Jun 2020 09:06:41: 11000000 INFO @ Tue, 16 Jun 2020 09:06:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:47: 6000000 INFO @ Tue, 16 Jun 2020 09:06:47: 12000000 INFO @ Tue, 16 Jun 2020 09:06:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:06:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:06:53: #1 total tags in treatment: 12933623 INFO @ Tue, 16 Jun 2020 09:06:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:53: #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 09:06:53: #1 tags after filtering in treatment: 12933623 INFO @ Tue, 16 Jun 2020 09:06:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:53: 7000000 INFO @ Tue, 16 Jun 2020 09:06:54: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:06:54: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:06:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:54: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:06:54: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 09:06:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.10_model.r WARNING @ Tue, 16 Jun 2020 09:06:54: #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 09:06:54: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 09:06:54: #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 09:06:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:06:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.05_summits.bed INFO @ Tue, 16 Jun 2020 09:06:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:59: 8000000 INFO @ Tue, 16 Jun 2020 09:07:06: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:07:12: 10000000 INFO @ Tue, 16 Jun 2020 09:07:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:18: 11000000 INFO @ Tue, 16 Jun 2020 09:07:24: 12000000 INFO @ Tue, 16 Jun 2020 09:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.10_summits.bed INFO @ Tue, 16 Jun 2020 09:07:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:07:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:07:30: #1 total tags in treatment: 12933623 INFO @ Tue, 16 Jun 2020 09:07:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:30: #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 09:07:31: #1 tags after filtering in treatment: 12933623 INFO @ Tue, 16 Jun 2020 09:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:32: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:07:32: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:32: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:07:32: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 09:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.20_model.r WARNING @ Tue, 16 Jun 2020 09:07:32: #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 09:07:32: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 09:07:32: #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 09:07:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:07:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466581/SRX466581.20_summits.bed INFO @ Tue, 16 Jun 2020 09:08:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling