Job ID = 6456274 SRX = SRX331423 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:51:46 prefetch.2.10.7: 1) Downloading 'SRR947660'... 2020-06-21T10:51:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:56:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:56:08 prefetch.2.10.7: 1) 'SRR947660' was downloaded successfully Read 17509655 spots for SRR947660/SRR947660.sra Written 17509655 spots for SRR947660/SRR947660.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: 00:04:54 17509655 reads; of these: 17509655 (100.00%) were unpaired; of these: 1535132 (8.77%) aligned 0 times 11617788 (66.35%) aligned exactly 1 time 4356735 (24.88%) aligned >1 times 91.23% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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] 4490787 / 15974523 = 0.2811 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 20:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.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 20:07:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:16: 1000000 INFO @ Sun, 21 Jun 2020 20:07:22: 2000000 INFO @ Sun, 21 Jun 2020 20:07:28: 3000000 INFO @ Sun, 21 Jun 2020 20:07:35: 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 20:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.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 20:07:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:41: 5000000 INFO @ Sun, 21 Jun 2020 20:07:47: 6000000 INFO @ Sun, 21 Jun 2020 20:07:47: 1000000 INFO @ Sun, 21 Jun 2020 20:07:54: 7000000 INFO @ Sun, 21 Jun 2020 20:07:55: 2000000 INFO @ Sun, 21 Jun 2020 20:08:00: 8000000 INFO @ Sun, 21 Jun 2020 20:08:02: 3000000 INFO @ Sun, 21 Jun 2020 20:08:07: 9000000 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 20:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.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 20:08:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:08:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:10: 4000000 INFO @ Sun, 21 Jun 2020 20:08:14: 10000000 INFO @ Sun, 21 Jun 2020 20:08:17: 1000000 INFO @ Sun, 21 Jun 2020 20:08:17: 5000000 INFO @ Sun, 21 Jun 2020 20:08:21: 11000000 INFO @ Sun, 21 Jun 2020 20:08:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:08:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:08:24: #1 total tags in treatment: 11483736 INFO @ Sun, 21 Jun 2020 20:08:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:24: #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 20:08:25: 2000000 INFO @ Sun, 21 Jun 2020 20:08:25: #1 tags after filtering in treatment: 11483735 INFO @ Sun, 21 Jun 2020 20:08:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:25: 6000000 INFO @ Sun, 21 Jun 2020 20:08:26: #2 number of paired peaks: 5471 INFO @ Sun, 21 Jun 2020 20:08:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:26: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 20:08:26: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 20:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.05_model.r INFO @ Sun, 21 Jun 2020 20:08:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:31: 3000000 INFO @ Sun, 21 Jun 2020 20:08:32: 7000000 INFO @ Sun, 21 Jun 2020 20:08:38: 4000000 INFO @ Sun, 21 Jun 2020 20:08:39: 8000000 INFO @ Sun, 21 Jun 2020 20:08:45: 5000000 INFO @ Sun, 21 Jun 2020 20:08:46: 9000000 INFO @ Sun, 21 Jun 2020 20:08:52: 6000000 INFO @ Sun, 21 Jun 2020 20:08:54: 10000000 INFO @ Sun, 21 Jun 2020 20:08:59: 7000000 INFO @ Sun, 21 Jun 2020 20:09:01: 11000000 INFO @ Sun, 21 Jun 2020 20:09:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:09:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:09:04: #1 total tags in treatment: 11483736 INFO @ Sun, 21 Jun 2020 20:09:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:04: #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 20:09:05: #1 tags after filtering in treatment: 11483735 INFO @ Sun, 21 Jun 2020 20:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:06: 8000000 INFO @ Sun, 21 Jun 2020 20:09:06: #2 number of paired peaks: 5471 INFO @ Sun, 21 Jun 2020 20:09:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:07: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 20:09:07: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 20:09:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.10_model.r INFO @ Sun, 21 Jun 2020 20:09:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:09:12: 9000000 INFO @ Sun, 21 Jun 2020 20:09:19: 10000000 INFO @ Sun, 21 Jun 2020 20:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.05_summits.bed INFO @ Sun, 21 Jun 2020 20:09:20: Done! pass1 - making usageList (549 chroms): 2 millis pass2 - checking and writing primary data (7596 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:25: 11000000 INFO @ Sun, 21 Jun 2020 20:09:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:09:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:09:29: #1 total tags in treatment: 11483736 INFO @ Sun, 21 Jun 2020 20:09:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:29: #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 20:09:29: #1 tags after filtering in treatment: 11483735 INFO @ Sun, 21 Jun 2020 20:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:29: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:31: #2 number of paired peaks: 5471 INFO @ Sun, 21 Jun 2020 20:09:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:31: #2 predicted fragment length is 239 bps INFO @ Sun, 21 Jun 2020 20:09:31: #2 alternative fragment length(s) may be 239 bps INFO @ Sun, 21 Jun 2020 20:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.20_model.r INFO @ Sun, 21 Jun 2020 20:09:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:09:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.10_summits.bed INFO @ Sun, 21 Jun 2020 20:10:00: Done! pass1 - making usageList (475 chroms): 2 millis pass2 - checking and writing primary data (6259 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:10:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331423/SRX331423.20_summits.bed INFO @ Sun, 21 Jun 2020 20:10:24: Done! pass1 - making usageList (348 chroms): 2 millis pass2 - checking and writing primary data (4731 records, 4 fields): 24 millis CompletedMACS2peakCalling