Job ID = 6457069 SRX = SRX4375833 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:20:09 prefetch.2.10.7: 1) Downloading 'SRR7506487'... 2020-06-21T11:20:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:21:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:21:23 prefetch.2.10.7: 'SRR7506487' is valid 2020-06-21T11:21:23 prefetch.2.10.7: 1) 'SRR7506487' was downloaded successfully Read 6703161 spots for SRR7506487/SRR7506487.sra Written 6703161 spots for SRR7506487/SRR7506487.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: 00:00:41 6703161 reads; of these: 6703161 (100.00%) were unpaired; of these: 5101181 (76.10%) aligned 0 times 1321357 (19.71%) aligned exactly 1 time 280623 (4.19%) aligned >1 times 23.90% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 302105 / 1601980 = 0.1886 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 20:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.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 20:23:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:30: 1000000 INFO @ Sun, 21 Jun 2020 20:23:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:23:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:23:32: #1 total tags in treatment: 1299875 INFO @ Sun, 21 Jun 2020 20:23:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:23:32: #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 20:23:32: #1 tags after filtering in treatment: 1299383 INFO @ Sun, 21 Jun 2020 20:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:23:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:23:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:23:33: #2 number of paired peaks: 4570 INFO @ Sun, 21 Jun 2020 20:23:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:23:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:23:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:23:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:23:33: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 20:23:33: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 21 Jun 2020 20:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.05_model.r INFO @ Sun, 21 Jun 2020 20:23:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:23:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.05_summits.bed INFO @ Sun, 21 Jun 2020 20:23:38: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (4437 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 20:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.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 20:23:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:00: 1000000 INFO @ Sun, 21 Jun 2020 20:24:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:24:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:24:02: #1 total tags in treatment: 1299875 INFO @ Sun, 21 Jun 2020 20:24:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:24:02: #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 20:24:02: #1 tags after filtering in treatment: 1299383 INFO @ Sun, 21 Jun 2020 20:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:24:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:24:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:24:03: #2 number of paired peaks: 4570 INFO @ Sun, 21 Jun 2020 20:24:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:24:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:24:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:24:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:24:03: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 20:24:03: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 21 Jun 2020 20:24:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.10_model.r INFO @ Sun, 21 Jun 2020 20:24:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:24:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:24:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.10_summits.bed INFO @ Sun, 21 Jun 2020 20:24:08: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (3183 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 20:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.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 20:24:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:22: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:24:28: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:24:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:24:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:24:31: #1 total tags in treatment: 1299875 INFO @ Sun, 21 Jun 2020 20:24:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:24:31: #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 20:24:31: #1 tags after filtering in treatment: 1299383 INFO @ Sun, 21 Jun 2020 20:24:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:24:31: #1 finished! INFO @ Sun, 21 Jun 2020 20:24:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:24:31: #2 number of paired peaks: 4570 INFO @ Sun, 21 Jun 2020 20:24:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:24:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:24:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:24:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:24:31: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 20:24:31: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 21 Jun 2020 20:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.20_model.r INFO @ Sun, 21 Jun 2020 20:24:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:24:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375833/SRX4375833.20_summits.bed INFO @ Sun, 21 Jun 2020 20:24:37: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (2124 records, 4 fields): 4 millis CompletedMACS2peakCalling