Job ID = 6454098 SRX = SRX181440 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:03:49 prefetch.2.10.7: 1) Downloading 'SRR548177'... 2020-06-21T09:03:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:06:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:06:08 prefetch.2.10.7: 1) 'SRR548177' was downloaded successfully Read 32097522 spots for SRR548177/SRR548177.sra Written 32097522 spots for SRR548177/SRR548177.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: 00:05:40 32097522 reads; of these: 32097522 (100.00%) were unpaired; of these: 4985743 (15.53%) aligned 0 times 23995568 (74.76%) aligned exactly 1 time 3116211 (9.71%) aligned >1 times 84.47% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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 8 files... [bam_rmdupse_core] 18994006 / 27111779 = 0.7006 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 18:17:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.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 18:17:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:32: 1000000 INFO @ Sun, 21 Jun 2020 18:17:36: 2000000 INFO @ Sun, 21 Jun 2020 18:17:41: 3000000 INFO @ Sun, 21 Jun 2020 18:17:45: 4000000 INFO @ Sun, 21 Jun 2020 18:17:49: 5000000 INFO @ Sun, 21 Jun 2020 18:17:54: 6000000 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 18:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.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 18:17:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:59: 7000000 INFO @ Sun, 21 Jun 2020 18:18:02: 1000000 INFO @ Sun, 21 Jun 2020 18:18:03: 8000000 INFO @ Sun, 21 Jun 2020 18:18:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:18:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:18:04: #1 total tags in treatment: 8117773 INFO @ Sun, 21 Jun 2020 18:18:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:04: #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 18:18:04: #1 tags after filtering in treatment: 8117731 INFO @ Sun, 21 Jun 2020 18:18:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:05: #2 number of paired peaks: 3300 INFO @ Sun, 21 Jun 2020 18:18:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:05: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:18:05: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 18:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.05_model.r INFO @ Sun, 21 Jun 2020 18:18:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:07: 2000000 INFO @ Sun, 21 Jun 2020 18:18:11: 3000000 INFO @ Sun, 21 Jun 2020 18:18:15: 4000000 INFO @ Sun, 21 Jun 2020 18:18:20: 5000000 INFO @ Sun, 21 Jun 2020 18:18:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:24: 6000000 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 18:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.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 18:18:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:29: 7000000 INFO @ Sun, 21 Jun 2020 18:18:32: 1000000 INFO @ Sun, 21 Jun 2020 18:18:34: 8000000 INFO @ Sun, 21 Jun 2020 18:18:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.05_summits.bed INFO @ Sun, 21 Jun 2020 18:18:35: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:18:35: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:18:35: #1 total tags in treatment: 8117773 INFO @ Sun, 21 Jun 2020 18:18:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:35: #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 18:18:35: Done! pass1 - making usageList (487 chroms): 2 millis INFO @ Sun, 21 Jun 2020 18:18:35: #1 tags after filtering in treatment: 8117731 INFO @ Sun, 21 Jun 2020 18:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:35: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (8915 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:36: #2 number of paired peaks: 3300 INFO @ Sun, 21 Jun 2020 18:18:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:36: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:18:36: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 18:18:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.10_model.r INFO @ Sun, 21 Jun 2020 18:18:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:37: 2000000 INFO @ Sun, 21 Jun 2020 18:18:41: 3000000 INFO @ Sun, 21 Jun 2020 18:18:46: 4000000 INFO @ Sun, 21 Jun 2020 18:18:50: 5000000 INFO @ Sun, 21 Jun 2020 18:18:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:54: 6000000 INFO @ Sun, 21 Jun 2020 18:18:59: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:19:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.10_summits.bed INFO @ Sun, 21 Jun 2020 18:19:03: Done! INFO @ Sun, 21 Jun 2020 18:19:04: 8000000 pass1 - making usageList (455 chroms): 2 millis pass2 - checking and writing primary data (5636 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:19:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:19:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:19:04: #1 total tags in treatment: 8117773 INFO @ Sun, 21 Jun 2020 18:19:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:04: #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 18:19:05: #1 tags after filtering in treatment: 8117731 INFO @ Sun, 21 Jun 2020 18:19:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:05: #2 number of paired peaks: 3300 INFO @ Sun, 21 Jun 2020 18:19:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:06: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:19:06: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 18:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.20_model.r INFO @ Sun, 21 Jun 2020 18:19:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:19:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181440/SRX181440.20_summits.bed INFO @ Sun, 21 Jun 2020 18:19:34: Done! pass1 - making usageList (406 chroms): 2 millis pass2 - checking and writing primary data (2534 records, 4 fields): 13 millis CompletedMACS2peakCalling