Job ID = 6454153 SRX = SRX1840072 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:02:34 prefetch.2.10.7: 1) Downloading 'SRR3661298'... 2020-06-21T09:02:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:06:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:06:28 prefetch.2.10.7: 1) 'SRR3661298' was downloaded successfully Read 9523883 spots for SRR3661298/SRR3661298.sra Written 9523883 spots for SRR3661298/SRR3661298.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: 00:05:27 9523883 reads; of these: 9523883 (100.00%) were unpaired; of these: 2470183 (25.94%) aligned 0 times 4549279 (47.77%) aligned exactly 1 time 2504421 (26.30%) aligned >1 times 74.06% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 2761603 / 7053700 = 0.3915 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 18:16:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.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 18:16:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:17: 1000000 INFO @ Sun, 21 Jun 2020 18:16:23: 2000000 INFO @ Sun, 21 Jun 2020 18:16:30: 3000000 INFO @ Sun, 21 Jun 2020 18:16:37: 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 @ Sun, 21 Jun 2020 18:16:39: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:16:39: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:16:39: #1 total tags in treatment: 4292097 INFO @ Sun, 21 Jun 2020 18:16:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:39: #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 18:16:39: #1 tags after filtering in treatment: 4292076 INFO @ Sun, 21 Jun 2020 18:16:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:39: #2 number of paired peaks: 1078 INFO @ Sun, 21 Jun 2020 18:16:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:40: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 18:16:40: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 18:16:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.05_model.r WARNING @ Sun, 21 Jun 2020 18:16:40: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:16:40: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 18:16:40: #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 18:16:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.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 18:16:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:47: 1000000 INFO @ Sun, 21 Jun 2020 18:16:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:53: 2000000 INFO @ Sun, 21 Jun 2020 18:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.05_summits.bed INFO @ Sun, 21 Jun 2020 18:16:56: Done! pass1 - making usageList (629 chroms): 1 millis pass2 - checking and writing primary data (2102 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:17:00: 3000000 INFO @ Sun, 21 Jun 2020 18:17:06: 4000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 18:17:09: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:17:09: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:17:09: #1 total tags in treatment: 4292097 INFO @ Sun, 21 Jun 2020 18:17:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 18:17:09: #1 tags after filtering in treatment: 4292076 INFO @ Sun, 21 Jun 2020 18:17:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:09: #2 number of paired peaks: 1078 INFO @ Sun, 21 Jun 2020 18:17:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:09: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 18:17:09: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 18:17:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.10_model.r WARNING @ Sun, 21 Jun 2020 18:17:09: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:09: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 18:17:09: #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 18:17:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.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 18:17:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:18: 1000000 INFO @ Sun, 21 Jun 2020 18:17:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:24: 2000000 INFO @ Sun, 21 Jun 2020 18:17:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.10_summits.bed INFO @ Sun, 21 Jun 2020 18:17:25: Done! pass1 - making usageList (526 chroms): 2 millis pass2 - checking and writing primary data (1350 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:17:31: 3000000 INFO @ Sun, 21 Jun 2020 18:17:38: 4000000 INFO @ Sun, 21 Jun 2020 18:17:40: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:17:40: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:17:40: #1 total tags in treatment: 4292097 INFO @ Sun, 21 Jun 2020 18:17:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:17:40: #1 tags after filtering in treatment: 4292076 INFO @ Sun, 21 Jun 2020 18:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:40: #2 number of paired peaks: 1078 INFO @ Sun, 21 Jun 2020 18:17:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:40: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 18:17:40: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 18:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.20_model.r WARNING @ Sun, 21 Jun 2020 18:17:40: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:40: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 18:17:40: #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 18:17:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:17:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840072/SRX1840072.20_summits.bed INFO @ Sun, 21 Jun 2020 18:17:56: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (776 records, 4 fields): 13 millis CompletedMACS2peakCalling