Job ID = 6454051 SRX = SRX1794235 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:43:19 prefetch.2.10.7: 1) Downloading 'SRR3575276'... 2020-06-21T08:43:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:44:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:44:33 prefetch.2.10.7: 'SRR3575276' is valid 2020-06-21T08:44:33 prefetch.2.10.7: 1) 'SRR3575276' was downloaded successfully Read 6589851 spots for SRR3575276/SRR3575276.sra Written 6589851 spots for SRR3575276/SRR3575276.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: 00:01:41 6589851 reads; of these: 6589851 (100.00%) were unpaired; of these: 374784 (5.69%) aligned 0 times 4919957 (74.66%) aligned exactly 1 time 1295110 (19.65%) aligned >1 times 94.31% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 799381 / 6215067 = 0.1286 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 17:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.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 17:48:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:47: 1000000 INFO @ Sun, 21 Jun 2020 17:48:53: 2000000 INFO @ Sun, 21 Jun 2020 17:49:00: 3000000 INFO @ Sun, 21 Jun 2020 17:49:06: 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 17:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.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 17:49:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:13: 5000000 INFO @ Sun, 21 Jun 2020 17:49:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:49:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:49:16: #1 total tags in treatment: 5415686 INFO @ Sun, 21 Jun 2020 17:49:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:16: #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 17:49:16: #1 tags after filtering in treatment: 5415505 INFO @ Sun, 21 Jun 2020 17:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:17: #2 number of paired peaks: 4169 INFO @ Sun, 21 Jun 2020 17:49:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:17: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 17:49:17: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 17:49:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.05_model.r INFO @ Sun, 21 Jun 2020 17:49:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:19: 1000000 INFO @ Sun, 21 Jun 2020 17:49:27: 2000000 INFO @ Sun, 21 Jun 2020 17:49:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:36: 3000000 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 17:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:40: Done! pass1 - making usageList (401 chroms): 2 millis pass2 - checking and writing primary data (7132 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.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 17:49:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:44: 4000000 INFO @ Sun, 21 Jun 2020 17:49:50: 1000000 INFO @ Sun, 21 Jun 2020 17:49:53: 5000000 INFO @ Sun, 21 Jun 2020 17:49:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:49:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:49:57: #1 total tags in treatment: 5415686 INFO @ Sun, 21 Jun 2020 17:49:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:57: #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 17:49:57: #1 tags after filtering in treatment: 5415505 INFO @ Sun, 21 Jun 2020 17:49:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:58: #2 number of paired peaks: 4169 INFO @ Sun, 21 Jun 2020 17:49:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:58: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 17:49:58: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 17:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.10_model.r INFO @ Sun, 21 Jun 2020 17:49:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:58: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:50:06: 3000000 INFO @ Sun, 21 Jun 2020 17:50:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:14: 4000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.10_summits.bed INFO @ Sun, 21 Jun 2020 17:50:21: Done! pass1 - making usageList (230 chroms): 2 millis pass2 - checking and writing primary data (5259 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:22: 5000000 INFO @ Sun, 21 Jun 2020 17:50:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:25: #1 total tags in treatment: 5415686 INFO @ Sun, 21 Jun 2020 17:50:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:25: #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 17:50:25: #1 tags after filtering in treatment: 5415505 INFO @ Sun, 21 Jun 2020 17:50:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:25: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:26: #2 number of paired peaks: 4169 INFO @ Sun, 21 Jun 2020 17:50:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:26: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 17:50:26: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 17:50:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.20_model.r INFO @ Sun, 21 Jun 2020 17:50:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794235/SRX1794235.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:48: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (3643 records, 4 fields): 9 millis CompletedMACS2peakCalling