Job ID = 6368612 SRX = SRX5020837 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:50 prefetch.2.10.7: 1) Downloading 'SRR8201460'... 2020-06-16T00:13:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:22 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:23 prefetch.2.10.7: 'SRR8201460' is valid 2020-06-16T00:15:23 prefetch.2.10.7: 1) 'SRR8201460' was downloaded successfully Read 16311814 spots for SRR8201460/SRR8201460.sra Written 16311814 spots for SRR8201460/SRR8201460.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: 00:03:47 16311814 reads; of these: 16311814 (100.00%) were unpaired; of these: 562105 (3.45%) aligned 0 times 12340889 (75.66%) aligned exactly 1 time 3408820 (20.90%) aligned >1 times 96.55% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 2794949 / 15749709 = 0.1775 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 09:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.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 09:24:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:08: 1000000 INFO @ Tue, 16 Jun 2020 09:24:13: 2000000 INFO @ Tue, 16 Jun 2020 09:24:18: 3000000 INFO @ Tue, 16 Jun 2020 09:24:24: 4000000 INFO @ Tue, 16 Jun 2020 09:24:29: 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 09:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.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 09:24:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:35: 6000000 INFO @ Tue, 16 Jun 2020 09:24:38: 1000000 INFO @ Tue, 16 Jun 2020 09:24:41: 7000000 INFO @ Tue, 16 Jun 2020 09:24:44: 2000000 INFO @ Tue, 16 Jun 2020 09:24:47: 8000000 INFO @ Tue, 16 Jun 2020 09:24:51: 3000000 INFO @ Tue, 16 Jun 2020 09:24:52: 9000000 INFO @ Tue, 16 Jun 2020 09:24:57: 4000000 INFO @ Tue, 16 Jun 2020 09:24:58: 10000000 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 09:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.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 09:25:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:03: 5000000 INFO @ Tue, 16 Jun 2020 09:25:04: 11000000 INFO @ Tue, 16 Jun 2020 09:25:08: 1000000 INFO @ Tue, 16 Jun 2020 09:25:09: 6000000 INFO @ Tue, 16 Jun 2020 09:25:10: 12000000 INFO @ Tue, 16 Jun 2020 09:25:14: 2000000 INFO @ Tue, 16 Jun 2020 09:25:16: 7000000 INFO @ Tue, 16 Jun 2020 09:25:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:25:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:25:16: #1 total tags in treatment: 12954760 INFO @ Tue, 16 Jun 2020 09:25:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:16: #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 09:25:16: #1 tags after filtering in treatment: 12954760 INFO @ Tue, 16 Jun 2020 09:25:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:17: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:25:17: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:17: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:25:17: #2 alternative fragment length(s) may be 2,42,570 bps INFO @ Tue, 16 Jun 2020 09:25:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.05_model.r WARNING @ Tue, 16 Jun 2020 09:25:17: #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 09:25:17: #2 You may need to consider one of the other alternative d(s): 2,42,570 WARNING @ Tue, 16 Jun 2020 09:25:17: #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 09:25:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:20: 3000000 INFO @ Tue, 16 Jun 2020 09:25:22: 8000000 INFO @ Tue, 16 Jun 2020 09:25:26: 4000000 INFO @ Tue, 16 Jun 2020 09:25:28: 9000000 INFO @ Tue, 16 Jun 2020 09:25:32: 5000000 INFO @ Tue, 16 Jun 2020 09:25:34: 10000000 INFO @ Tue, 16 Jun 2020 09:25:38: 6000000 INFO @ Tue, 16 Jun 2020 09:25:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:40: 11000000 INFO @ Tue, 16 Jun 2020 09:25:44: 7000000 INFO @ Tue, 16 Jun 2020 09:25:46: 12000000 INFO @ Tue, 16 Jun 2020 09:25:50: 8000000 INFO @ Tue, 16 Jun 2020 09:25:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:25:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:25:52: #1 total tags in treatment: 12954760 INFO @ Tue, 16 Jun 2020 09:25:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:52: #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 09:25:52: #1 tags after filtering in treatment: 12954760 INFO @ Tue, 16 Jun 2020 09:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:53: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:25:53: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:53: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:25:53: #2 alternative fragment length(s) may be 2,42,570 bps INFO @ Tue, 16 Jun 2020 09:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.10_model.r WARNING @ Tue, 16 Jun 2020 09:25:53: #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 09:25:53: #2 You may need to consider one of the other alternative d(s): 2,42,570 WARNING @ Tue, 16 Jun 2020 09:25:53: #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 09:25:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:56: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:01: 10000000 INFO @ Tue, 16 Jun 2020 09:26:06: 11000000 INFO @ Tue, 16 Jun 2020 09:26:12: 12000000 INFO @ Tue, 16 Jun 2020 09:26:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:26:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:26:17: #1 total tags in treatment: 12954760 INFO @ Tue, 16 Jun 2020 09:26:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:17: #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 09:26:17: #1 tags after filtering in treatment: 12954760 INFO @ Tue, 16 Jun 2020 09:26:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:18: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:26:18: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:18: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:26:18: #2 alternative fragment length(s) may be 2,42,570 bps INFO @ Tue, 16 Jun 2020 09:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.20_model.r WARNING @ Tue, 16 Jun 2020 09:26:18: #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 09:26:18: #2 You may need to consider one of the other alternative d(s): 2,42,570 WARNING @ Tue, 16 Jun 2020 09:26:18: #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 09:26:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:25: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020837/SRX5020837.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling