Job ID = 6454307 SRX = SRX197578 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:05:24 prefetch.2.10.7: 1) Downloading 'SRR597006'... 2020-06-21T09:05:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:07:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:07:47 prefetch.2.10.7: 'SRR597006' is valid 2020-06-21T09:07:47 prefetch.2.10.7: 1) 'SRR597006' was downloaded successfully Read 24521366 spots for SRR597006/SRR597006.sra Written 24521366 spots for SRR597006/SRR597006.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: 00:03:51 24521366 reads; of these: 24521366 (100.00%) were unpaired; of these: 10917215 (44.52%) aligned 0 times 10876817 (44.36%) aligned exactly 1 time 2727334 (11.12%) aligned >1 times 55.48% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 8056973 / 13604151 = 0.5922 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 18:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.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 18:15:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:23: 1000000 INFO @ Sun, 21 Jun 2020 18:15:28: 2000000 INFO @ Sun, 21 Jun 2020 18:15:33: 3000000 INFO @ Sun, 21 Jun 2020 18:15:37: 4000000 INFO @ Sun, 21 Jun 2020 18:15:42: 5000000 INFO @ Sun, 21 Jun 2020 18:15:45: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:15:45: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:15:45: #1 total tags in treatment: 5547178 INFO @ Sun, 21 Jun 2020 18:15:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:45: #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 18:15:46: #1 tags after filtering in treatment: 5547175 INFO @ Sun, 21 Jun 2020 18:15:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:46: #2 number of paired peaks: 1004 INFO @ Sun, 21 Jun 2020 18:15:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:46: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 18:15:46: #2 alternative fragment length(s) may be 3,35,551 bps INFO @ Sun, 21 Jun 2020 18:15:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.05_model.r WARNING @ Sun, 21 Jun 2020 18:15:46: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:15:46: #2 You may need to consider one of the other alternative d(s): 3,35,551 WARNING @ Sun, 21 Jun 2020 18:15:46: #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 18:15:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:46: #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 18:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.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 18:15:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:53: 1000000 INFO @ Sun, 21 Jun 2020 18:15:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:58: 2000000 INFO @ Sun, 21 Jun 2020 18:16:03: 3000000 INFO @ Sun, 21 Jun 2020 18:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.05_summits.bed INFO @ Sun, 21 Jun 2020 18:16:03: Done! pass1 - making usageList (507 chroms): 2 millis pass2 - checking and writing primary data (2397 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:16:08: 4000000 INFO @ Sun, 21 Jun 2020 18:16:13: 5000000 INFO @ Sun, 21 Jun 2020 18:16:16: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:16:16: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:16:16: #1 total tags in treatment: 5547178 INFO @ Sun, 21 Jun 2020 18:16:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:16: #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 18:16:16: #1 tags after filtering in treatment: 5547175 INFO @ Sun, 21 Jun 2020 18:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:16: #2 number of paired peaks: 1004 INFO @ Sun, 21 Jun 2020 18:16:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:16: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 18:16:16: #2 alternative fragment length(s) may be 3,35,551 bps INFO @ Sun, 21 Jun 2020 18:16:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.10_model.r WARNING @ Sun, 21 Jun 2020 18:16:16: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:16:16: #2 You may need to consider one of the other alternative d(s): 3,35,551 WARNING @ Sun, 21 Jun 2020 18:16:16: #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 18:16:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:16: #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 18:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.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 18:16:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:23: 1000000 INFO @ Sun, 21 Jun 2020 18:16:28: 2000000 INFO @ Sun, 21 Jun 2020 18:16:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:33: 3000000 INFO @ Sun, 21 Jun 2020 18:16:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.10_summits.bed INFO @ Sun, 21 Jun 2020 18:16:34: Done! pass1 - making usageList (354 chroms): 1 millis pass2 - checking and writing primary data (960 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:16:38: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:16:43: 5000000 INFO @ Sun, 21 Jun 2020 18:16:46: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:16:46: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:16:46: #1 total tags in treatment: 5547178 INFO @ Sun, 21 Jun 2020 18:16:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:46: #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 18:16:46: #1 tags after filtering in treatment: 5547175 INFO @ Sun, 21 Jun 2020 18:16:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:46: #2 number of paired peaks: 1004 INFO @ Sun, 21 Jun 2020 18:16:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:46: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 18:16:46: #2 alternative fragment length(s) may be 3,35,551 bps INFO @ Sun, 21 Jun 2020 18:16:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.20_model.r WARNING @ Sun, 21 Jun 2020 18:16:46: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:16:46: #2 You may need to consider one of the other alternative d(s): 3,35,551 WARNING @ Sun, 21 Jun 2020 18:16:46: #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 18:16:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:16:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197578/SRX197578.20_summits.bed INFO @ Sun, 21 Jun 2020 18:17:03: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 4 millis CompletedMACS2peakCalling