Job ID = 6457176 SRX = SRX4520670 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:34:10 prefetch.2.10.7: 1) Downloading 'SRR7659068'... 2020-06-21T11:34:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:37:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:37:18 prefetch.2.10.7: 'SRR7659068' is valid 2020-06-21T11:37:18 prefetch.2.10.7: 1) 'SRR7659068' was downloaded successfully 2020-06-21T11:37:18 prefetch.2.10.7: 'SRR7659068' has 0 unresolved dependencies Read 9630859 spots for SRR7659068/SRR7659068.sra Written 9630859 spots for SRR7659068/SRR7659068.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: 00:02:26 9630859 reads; of these: 9630859 (100.00%) were unpaired; of these: 1493503 (15.51%) aligned 0 times 5475792 (56.86%) aligned exactly 1 time 2661564 (27.64%) aligned >1 times 84.49% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 1233990 / 8137356 = 0.1516 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 20:43:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.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 20:43:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:13: 1000000 INFO @ Sun, 21 Jun 2020 20:43:18: 2000000 INFO @ Sun, 21 Jun 2020 20:43:23: 3000000 INFO @ Sun, 21 Jun 2020 20:43:28: 4000000 INFO @ Sun, 21 Jun 2020 20:43:32: 5000000 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 20:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.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 20:43:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:38: 6000000 INFO @ Sun, 21 Jun 2020 20:43:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:43:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:43:43: #1 total tags in treatment: 6903366 INFO @ Sun, 21 Jun 2020 20:43:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:43: #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 20:43:43: 1000000 INFO @ Sun, 21 Jun 2020 20:43:43: #1 tags after filtering in treatment: 6903249 INFO @ Sun, 21 Jun 2020 20:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:44: #2 number of paired peaks: 2060 INFO @ Sun, 21 Jun 2020 20:43:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:44: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:44: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:44: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:44: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 20:43:44: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 20:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.05_model.r INFO @ Sun, 21 Jun 2020 20:43:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:48: 2000000 INFO @ Sun, 21 Jun 2020 20:43:53: 3000000 INFO @ Sun, 21 Jun 2020 20:43:58: 4000000 INFO @ Sun, 21 Jun 2020 20:44:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:03: 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 20:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.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 20:44:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:08: 6000000 INFO @ Sun, 21 Jun 2020 20:44:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.05_summits.bed INFO @ Sun, 21 Jun 2020 20:44:09: Done! pass1 - making usageList (594 chroms): 1 millis pass2 - checking and writing primary data (3643 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:13: 1000000 INFO @ Sun, 21 Jun 2020 20:44:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:44:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:44:13: #1 total tags in treatment: 6903366 INFO @ Sun, 21 Jun 2020 20:44:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:13: #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 20:44:14: #1 tags after filtering in treatment: 6903249 INFO @ Sun, 21 Jun 2020 20:44:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:14: #2 number of paired peaks: 2060 INFO @ Sun, 21 Jun 2020 20:44:14: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:14: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 20:44:14: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 20:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.10_model.r INFO @ Sun, 21 Jun 2020 20:44:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:18: 2000000 INFO @ Sun, 21 Jun 2020 20:44:23: 3000000 INFO @ Sun, 21 Jun 2020 20:44:28: 4000000 INFO @ Sun, 21 Jun 2020 20:44:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:33: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:44:39: 6000000 INFO @ Sun, 21 Jun 2020 20:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.10_summits.bed INFO @ Sun, 21 Jun 2020 20:44:39: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (2449 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:44:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:44:43: #1 total tags in treatment: 6903366 INFO @ Sun, 21 Jun 2020 20:44:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:43: #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 20:44:44: #1 tags after filtering in treatment: 6903249 INFO @ Sun, 21 Jun 2020 20:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:44: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:44: #2 number of paired peaks: 2060 INFO @ Sun, 21 Jun 2020 20:44:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:44: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:44: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:44: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:44: #2 predicted fragment length is 188 bps INFO @ Sun, 21 Jun 2020 20:44:44: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 21 Jun 2020 20:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.20_model.r INFO @ Sun, 21 Jun 2020 20:44:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:45:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4520670/SRX4520670.20_summits.bed INFO @ Sun, 21 Jun 2020 20:45:09: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (1462 records, 4 fields): 12 millis CompletedMACS2peakCalling