Job ID = 6367677 SRX = SRX3862416 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:37:14 prefetch.2.10.7: 1) Downloading 'SRR6914653'... 2020-06-15T23:37:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:36 prefetch.2.10.7: 1) 'SRR6914653' was downloaded successfully 2020-06-15T23:41:36 prefetch.2.10.7: 'SRR6914653' has 0 unresolved dependencies Read 20468883 spots for SRR6914653/SRR6914653.sra Written 20468883 spots for SRR6914653/SRR6914653.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:02 20468883 reads; of these: 20468883 (100.00%) were unpaired; of these: 8870697 (43.34%) aligned 0 times 9750066 (47.63%) aligned exactly 1 time 1848120 (9.03%) aligned >1 times 56.66% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 10528247 / 11598186 = 0.9077 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 08:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.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 08:50:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:18: 1000000 INFO @ Tue, 16 Jun 2020 08:50:18: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:50:18: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:50:18: #1 total tags in treatment: 1069939 INFO @ Tue, 16 Jun 2020 08:50:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:18: #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 08:50:18: #1 tags after filtering in treatment: 1069939 INFO @ Tue, 16 Jun 2020 08:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:18: #2 number of paired peaks: 1165 INFO @ Tue, 16 Jun 2020 08:50:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:18: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:50:18: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 16 Jun 2020 08:50:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.05_model.r WARNING @ Tue, 16 Jun 2020 08:50:18: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:18: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 16 Jun 2020 08:50:18: #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 08:50:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:50:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.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 08:50:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:48: 1000000 INFO @ Tue, 16 Jun 2020 08:50:48: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:50:48: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:50:48: #1 total tags in treatment: 1069939 INFO @ Tue, 16 Jun 2020 08:50:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:48: #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 08:50:48: #1 tags after filtering in treatment: 1069939 INFO @ Tue, 16 Jun 2020 08:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:48: #2 number of paired peaks: 1165 INFO @ Tue, 16 Jun 2020 08:50:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:48: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:50:48: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 16 Jun 2020 08:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:48: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:48: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 16 Jun 2020 08:50:48: #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 08:50:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (320 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.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 08:51:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:11: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:18: 1000000 INFO @ Tue, 16 Jun 2020 08:51:18: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:51:18: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:51:18: #1 total tags in treatment: 1069939 INFO @ Tue, 16 Jun 2020 08:51:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:18: #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 08:51:18: #1 tags after filtering in treatment: 1069939 INFO @ Tue, 16 Jun 2020 08:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:18: #2 number of paired peaks: 1165 INFO @ Tue, 16 Jun 2020 08:51:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:18: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:51:18: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 16 Jun 2020 08:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:18: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:18: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 16 Jun 2020 08:51:18: #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 08:51:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862416/SRX3862416.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 1 millis CompletedMACS2peakCalling