Job ID = 6455149 SRX = SRX2788647 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:55 prefetch.2.10.7: 1) Downloading 'SRR5515267'... 2020-06-21T09:53:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:31 prefetch.2.10.7: 1) 'SRR5515267' was downloaded successfully 2020-06-21T10:24:31 prefetch.2.10.7: 'SRR5515267' has 0 unresolved dependencies Read 150601542 spots for SRR5515267/SRR5515267.sra Written 150601542 spots for SRR5515267/SRR5515267.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: 00:46:15 150601542 reads; of these: 150601542 (100.00%) were unpaired; of these: 51628534 (34.28%) aligned 0 times 85924717 (57.05%) aligned exactly 1 time 13048291 (8.66%) aligned >1 times 65.72% overall alignment rate Time searching: 00:46:15 Overall time: 00:46:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 44 files... [bam_rmdupse_core] 96028320 / 98973008 = 0.9702 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 @ Sun, 21 Jun 2020 20:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:46:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:46:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:46:36: 1000000 INFO @ Sun, 21 Jun 2020 20:46:42: 2000000 INFO @ Sun, 21 Jun 2020 20:46:50: #1 tag size is determined as 90 bps INFO @ Sun, 21 Jun 2020 20:46:50: #1 tag size = 90 INFO @ Sun, 21 Jun 2020 20:46:50: #1 total tags in treatment: 2944688 INFO @ Sun, 21 Jun 2020 20:46:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:46:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:46:50: #1 tags after filtering in treatment: 2944458 INFO @ Sun, 21 Jun 2020 20:46:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:46:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:46:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:46:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:46:51: #2 number of paired peaks: 6293 INFO @ Sun, 21 Jun 2020 20:46:51: start model_add_line... INFO @ Sun, 21 Jun 2020 20:46:51: start X-correlation... INFO @ Sun, 21 Jun 2020 20:46:51: end of X-cor INFO @ Sun, 21 Jun 2020 20:46:51: #2 finished! INFO @ Sun, 21 Jun 2020 20:46:51: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 20:46:51: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 20:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.05_model.r WARNING @ Sun, 21 Jun 2020 20:46:51: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:46:51: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sun, 21 Jun 2020 20:46:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:46:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:46:51: #3 Pre-compute pvalue-qvalue table... 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 @ Sun, 21 Jun 2020 20:46:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:47:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.05_summits.bed INFO @ Sun, 21 Jun 2020 20:47:03: Done! pass1 - making usageList (396 chroms): 2 millis pass2 - checking and writing primary data (7052 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:47:08: 1000000 INFO @ Sun, 21 Jun 2020 20:47:16: 2000000 INFO @ Sun, 21 Jun 2020 20:47:25: #1 tag size is determined as 90 bps INFO @ Sun, 21 Jun 2020 20:47:25: #1 tag size = 90 INFO @ Sun, 21 Jun 2020 20:47:25: #1 total tags in treatment: 2944688 INFO @ Sun, 21 Jun 2020 20:47:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:47:25: #1 tags after filtering in treatment: 2944458 INFO @ Sun, 21 Jun 2020 20:47:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:26: #2 number of paired peaks: 6293 INFO @ Sun, 21 Jun 2020 20:47:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:26: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 20:47:26: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 20:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.10_model.r WARNING @ Sun, 21 Jun 2020 20:47:26: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:47:26: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sun, 21 Jun 2020 20:47:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:47:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:26: #3 Pre-compute pvalue-qvalue table... 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 @ Sun, 21 Jun 2020 20:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 20:47:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:47:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:47:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:47:38: 1000000 INFO @ Sun, 21 Jun 2020 20:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.10_summits.bed INFO @ Sun, 21 Jun 2020 20:47:39: Done! pass1 - making usageList (250 chroms): 2 millis pass2 - checking and writing primary data (4513 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:47:46: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:47:55: #1 tag size is determined as 90 bps INFO @ Sun, 21 Jun 2020 20:47:55: #1 tag size = 90 INFO @ Sun, 21 Jun 2020 20:47:55: #1 total tags in treatment: 2944688 INFO @ Sun, 21 Jun 2020 20:47:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:47:56: #1 tags after filtering in treatment: 2944458 INFO @ Sun, 21 Jun 2020 20:47:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:56: #2 number of paired peaks: 6293 INFO @ Sun, 21 Jun 2020 20:47:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:56: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:56: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:56: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:56: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 20:47:56: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 20:47:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.20_model.r WARNING @ Sun, 21 Jun 2020 20:47:56: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:47:56: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sun, 21 Jun 2020 20:47:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:47:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:48:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788647/SRX2788647.20_summits.bed INFO @ Sun, 21 Jun 2020 20:48:09: Done! pass1 - making usageList (153 chroms): 2 millis pass2 - checking and writing primary data (2840 records, 4 fields): 12 millis CompletedMACS2peakCalling