Job ID = 6458449 SRX = SRX5227003 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:22 prefetch.2.10.7: 1) Downloading 'SRR8417918'... 2020-06-21T12:31:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:32:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:32:13 prefetch.2.10.7: 'SRR8417918' is valid 2020-06-21T12:32:13 prefetch.2.10.7: 1) 'SRR8417918' was downloaded successfully 2020-06-21T12:32:13 prefetch.2.10.7: 'SRR8417918' has 0 unresolved dependencies Read 3998090 spots for SRR8417918/SRR8417918.sra Written 3998090 spots for SRR8417918/SRR8417918.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: 00:01:39 3998090 reads; of these: 3998090 (100.00%) were unpaired; of these: 322550 (8.07%) aligned 0 times 2543335 (63.61%) aligned exactly 1 time 1132205 (28.32%) aligned >1 times 91.93% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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_rmdupse_core] 298641 / 3675540 = 0.0813 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 21:35:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.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 21:35:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:55: 1000000 INFO @ Sun, 21 Jun 2020 21:36:02: 2000000 INFO @ Sun, 21 Jun 2020 21:36:08: 3000000 INFO @ Sun, 21 Jun 2020 21:36:11: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:36:11: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:36:11: #1 total tags in treatment: 3376899 INFO @ Sun, 21 Jun 2020 21:36:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:11: #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 21:36:11: #1 tags after filtering in treatment: 3376643 INFO @ Sun, 21 Jun 2020 21:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:11: #2 number of paired peaks: 1649 INFO @ Sun, 21 Jun 2020 21:36:11: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:12: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:36:12: #2 alternative fragment length(s) may be 91,579 bps INFO @ Sun, 21 Jun 2020 21:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.05_model.r WARNING @ Sun, 21 Jun 2020 21:36:12: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:12: #2 You may need to consider one of the other alternative d(s): 91,579 WARNING @ Sun, 21 Jun 2020 21:36:12: #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 21:36:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:12: #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 21:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.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 21:36:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.05_summits.bed INFO @ Sun, 21 Jun 2020 21:36:23: Done! pass1 - making usageList (387 chroms): 1 millis pass2 - checking and writing primary data (1216 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:25: 1000000 INFO @ Sun, 21 Jun 2020 21:36:32: 2000000 INFO @ Sun, 21 Jun 2020 21:36:39: 3000000 INFO @ Sun, 21 Jun 2020 21:36:41: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:36:41: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:36:41: #1 total tags in treatment: 3376899 INFO @ Sun, 21 Jun 2020 21:36:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:41: #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 21:36:41: #1 tags after filtering in treatment: 3376643 INFO @ Sun, 21 Jun 2020 21:36:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:42: #2 number of paired peaks: 1649 INFO @ Sun, 21 Jun 2020 21:36:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:42: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:36:42: #2 alternative fragment length(s) may be 91,579 bps INFO @ Sun, 21 Jun 2020 21:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.10_model.r WARNING @ Sun, 21 Jun 2020 21:36:42: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:42: #2 You may need to consider one of the other alternative d(s): 91,579 WARNING @ Sun, 21 Jun 2020 21:36:42: #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 21:36:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:42: #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 21:36:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.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 21:36:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.10_summits.bed INFO @ Sun, 21 Jun 2020 21:36:53: Done! pass1 - making usageList (215 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:56: 1000000 INFO @ Sun, 21 Jun 2020 21:37:02: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:37:09: 3000000 INFO @ Sun, 21 Jun 2020 21:37:12: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:37:12: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:37:12: #1 total tags in treatment: 3376899 INFO @ Sun, 21 Jun 2020 21:37:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:37:12: #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 21:37:12: #1 tags after filtering in treatment: 3376643 INFO @ Sun, 21 Jun 2020 21:37:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:37:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:37:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:37:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:37:12: #2 number of paired peaks: 1649 INFO @ Sun, 21 Jun 2020 21:37:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:37:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:37:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:37:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:37:12: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:37:12: #2 alternative fragment length(s) may be 91,579 bps INFO @ Sun, 21 Jun 2020 21:37:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.20_model.r WARNING @ Sun, 21 Jun 2020 21:37:12: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:37:12: #2 You may need to consider one of the other alternative d(s): 91,579 WARNING @ Sun, 21 Jun 2020 21:37:12: #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 21:37:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:37:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:37:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227003/SRX5227003.20_summits.bed INFO @ Sun, 21 Jun 2020 21:37:24: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 6 millis CompletedMACS2peakCalling