Job ID = 6452441 SRX = SRX013061 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:52:15 prefetch.2.10.7: 1) Downloading 'SRR030327'... 2020-06-21T07:52:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:53:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:53:26 prefetch.2.10.7: 'SRR030327' is valid 2020-06-21T07:53:26 prefetch.2.10.7: 1) 'SRR030327' was downloaded successfully Read 7780168 spots for SRR030327/SRR030327.sra Written 7780168 spots for SRR030327/SRR030327.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: 00:01:30 7780168 reads; of these: 7780168 (100.00%) were unpaired; of these: 344610 (4.43%) aligned 0 times 5864062 (75.37%) aligned exactly 1 time 1571496 (20.20%) aligned >1 times 95.57% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 1889469 / 7435558 = 0.2541 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 16:57:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.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 16:57:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:32: 1000000 INFO @ Sun, 21 Jun 2020 16:57:37: 2000000 INFO @ Sun, 21 Jun 2020 16:57:42: 3000000 INFO @ Sun, 21 Jun 2020 16:57:46: 4000000 INFO @ Sun, 21 Jun 2020 16:57:52: 5000000 INFO @ Sun, 21 Jun 2020 16:57:55: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:57:55: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:57:55: #1 total tags in treatment: 5546089 INFO @ Sun, 21 Jun 2020 16:57:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:55: #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 16:57:55: #1 tags after filtering in treatment: 5546042 INFO @ Sun, 21 Jun 2020 16:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:55: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:55: #2 looking for paired plus/minus strand peaks... 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 16:57:56: #2 number of paired peaks: 1462 INFO @ Sun, 21 Jun 2020 16:57:56: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:56: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:56: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:56: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:56: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 16:57:56: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 16:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.05_model.r INFO @ Sun, 21 Jun 2020 16:57:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.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 16:57:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:02: 1000000 INFO @ Sun, 21 Jun 2020 16:58:07: 2000000 INFO @ Sun, 21 Jun 2020 16:58:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:12: 3000000 INFO @ Sun, 21 Jun 2020 16:58:17: 4000000 INFO @ Sun, 21 Jun 2020 16:58:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.05_summits.bed INFO @ Sun, 21 Jun 2020 16:58:18: Done! pass1 - making usageList (261 chroms): 1 millis pass2 - checking and writing primary data (3489 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:58:22: 5000000 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 16:58:25: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:25: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:25: #1 total tags in treatment: 5546089 INFO @ Sun, 21 Jun 2020 16:58:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:25: #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 16:58:26: #1 tags after filtering in treatment: 5546042 INFO @ Sun, 21 Jun 2020 16:58:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:26: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:26: #2 number of paired peaks: 1462 INFO @ Sun, 21 Jun 2020 16:58:26: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:26: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:26: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:26: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:26: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 16:58:26: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 16:58:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.10_model.r INFO @ Sun, 21 Jun 2020 16:58:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.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 16:58:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:32: 1000000 INFO @ Sun, 21 Jun 2020 16:58:38: 2000000 INFO @ Sun, 21 Jun 2020 16:58:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:43: 3000000 INFO @ Sun, 21 Jun 2020 16:58:48: 4000000 INFO @ Sun, 21 Jun 2020 16:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.10_summits.bed INFO @ Sun, 21 Jun 2020 16:58:49: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (2138 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:58:54: 5000000 INFO @ Sun, 21 Jun 2020 16:58:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:57: #1 total tags in treatment: 5546089 INFO @ Sun, 21 Jun 2020 16:58:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:57: #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 16:58:57: #1 tags after filtering in treatment: 5546042 INFO @ Sun, 21 Jun 2020 16:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:57: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:58: #2 number of paired peaks: 1462 INFO @ Sun, 21 Jun 2020 16:58:58: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:58: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:58: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:58: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:58: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 16:58:58: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 16:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.20_model.r INFO @ Sun, 21 Jun 2020 16:58:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:59:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013061/SRX013061.20_summits.bed INFO @ Sun, 21 Jun 2020 16:59:21: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (1248 records, 4 fields): 7 millis CompletedMACS2peakCalling