Job ID = 6368115 SRX = SRX466578 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:03:00 prefetch.2.10.7: 1) Downloading 'SRR1163644'... 2020-06-16T00:03:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:04:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:04:37 prefetch.2.10.7: 'SRR1163644' is valid 2020-06-16T00:04:37 prefetch.2.10.7: 1) 'SRR1163644' was downloaded successfully Read 13129788 spots for SRR1163644/SRR1163644.sra Written 13129788 spots for SRR1163644/SRR1163644.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: 00:02:58 13129788 reads; of these: 13129788 (100.00%) were unpaired; of these: 270075 (2.06%) aligned 0 times 10628651 (80.95%) aligned exactly 1 time 2231062 (16.99%) aligned >1 times 97.94% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 2051644 / 12859713 = 0.1595 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 09:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.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 09:11:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:09: 1000000 INFO @ Tue, 16 Jun 2020 09:11:15: 2000000 INFO @ Tue, 16 Jun 2020 09:11:21: 3000000 INFO @ Tue, 16 Jun 2020 09:11:26: 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 09:11:32: 5000000 INFO @ Tue, 16 Jun 2020 09:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.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 09:11:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:38: 6000000 INFO @ Tue, 16 Jun 2020 09:11:40: 1000000 INFO @ Tue, 16 Jun 2020 09:11:45: 7000000 INFO @ Tue, 16 Jun 2020 09:11:47: 2000000 INFO @ Tue, 16 Jun 2020 09:11:51: 8000000 INFO @ Tue, 16 Jun 2020 09:11:53: 3000000 INFO @ Tue, 16 Jun 2020 09:11:57: 9000000 INFO @ Tue, 16 Jun 2020 09:11:59: 4000000 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 09:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.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 09:12:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:04: 10000000 INFO @ Tue, 16 Jun 2020 09:12:06: 5000000 INFO @ Tue, 16 Jun 2020 09:12:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:09: #1 total tags in treatment: 10808069 INFO @ Tue, 16 Jun 2020 09:12:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:09: #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 09:12:09: #1 tags after filtering in treatment: 10808069 INFO @ Tue, 16 Jun 2020 09:12:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:10: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 09:12:10: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:10: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:12:10: #2 alternative fragment length(s) may be 2,43,544,564 bps INFO @ Tue, 16 Jun 2020 09:12:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:10: #2 You may need to consider one of the other alternative d(s): 2,43,544,564 WARNING @ Tue, 16 Jun 2020 09:12:10: #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 09:12:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:10: 1000000 INFO @ Tue, 16 Jun 2020 09:12:13: 6000000 INFO @ Tue, 16 Jun 2020 09:12:17: 2000000 INFO @ Tue, 16 Jun 2020 09:12:19: 7000000 INFO @ Tue, 16 Jun 2020 09:12:23: 3000000 INFO @ Tue, 16 Jun 2020 09:12:26: 8000000 INFO @ Tue, 16 Jun 2020 09:12:30: 4000000 INFO @ Tue, 16 Jun 2020 09:12:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:32: 9000000 INFO @ Tue, 16 Jun 2020 09:12:36: 5000000 INFO @ Tue, 16 Jun 2020 09:12:38: 10000000 INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 1 millis INFO @ Tue, 16 Jun 2020 09:12:42: 6000000 CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:44: #1 total tags in treatment: 10808069 INFO @ Tue, 16 Jun 2020 09:12:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:44: #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 09:12:44: #1 tags after filtering in treatment: 10808069 INFO @ Tue, 16 Jun 2020 09:12:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:45: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 09:12:45: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:45: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:12:45: #2 alternative fragment length(s) may be 2,43,544,564 bps INFO @ Tue, 16 Jun 2020 09:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:45: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:45: #2 You may need to consider one of the other alternative d(s): 2,43,544,564 WARNING @ Tue, 16 Jun 2020 09:12:45: #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 09:12:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:49: 7000000 INFO @ Tue, 16 Jun 2020 09:12:55: 8000000 INFO @ Tue, 16 Jun 2020 09:13:00: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:06: 10000000 INFO @ Tue, 16 Jun 2020 09:13:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:13:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:13:11: #1 total tags in treatment: 10808069 INFO @ Tue, 16 Jun 2020 09:13:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:11: #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 09:13:11: #1 tags after filtering in treatment: 10808069 INFO @ Tue, 16 Jun 2020 09:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:12: #2 number of paired peaks: 372 WARNING @ Tue, 16 Jun 2020 09:13:12: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:12: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:13:12: #2 alternative fragment length(s) may be 2,43,544,564 bps INFO @ Tue, 16 Jun 2020 09:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:12: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:12: #2 You may need to consider one of the other alternative d(s): 2,43,544,564 WARNING @ Tue, 16 Jun 2020 09:13:12: #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 09:13:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (457 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466578/SRX466578.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling