Job ID = 6457256 SRX = SRX4580643 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:37:43 prefetch.2.10.7: 1) Downloading 'SRR7724136'... 2020-06-21T11:37:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:39:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:39:42 prefetch.2.10.7: 'SRR7724136' is valid 2020-06-21T11:39:42 prefetch.2.10.7: 1) 'SRR7724136' was downloaded successfully Read 10451179 spots for SRR7724136/SRR7724136.sra Written 10451179 spots for SRR7724136/SRR7724136.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: 00:02:34 10451179 reads; of these: 10451179 (100.00%) were unpaired; of these: 2999347 (28.70%) aligned 0 times 3385221 (32.39%) aligned exactly 1 time 4066611 (38.91%) aligned >1 times 71.30% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 1137456 / 7451832 = 0.1526 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 20:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.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 20:45:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:13: 1000000 INFO @ Sun, 21 Jun 2020 20:45:19: 2000000 INFO @ Sun, 21 Jun 2020 20:45:24: 3000000 INFO @ Sun, 21 Jun 2020 20:45:29: 4000000 INFO @ Sun, 21 Jun 2020 20:45:35: 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 20:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.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 20:45:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:41: 6000000 INFO @ Sun, 21 Jun 2020 20:45:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:45:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:45:43: #1 total tags in treatment: 6314376 INFO @ Sun, 21 Jun 2020 20:45:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:45:43: #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 20:45:44: #1 tags after filtering in treatment: 6314309 INFO @ Sun, 21 Jun 2020 20:45:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:45:44: #1 finished! INFO @ Sun, 21 Jun 2020 20:45:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:45:44: #2 number of paired peaks: 3560 INFO @ Sun, 21 Jun 2020 20:45:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:44: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:44: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:44: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:44: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:45:44: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 20:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.05_model.r WARNING @ Sun, 21 Jun 2020 20:45:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:45:45: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 20:45:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:45:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:45:45: 1000000 INFO @ Sun, 21 Jun 2020 20:45:52: 2000000 INFO @ Sun, 21 Jun 2020 20:45:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:58: 3000000 INFO @ Sun, 21 Jun 2020 20:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:46:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:46:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.05_summits.bed INFO @ Sun, 21 Jun 2020 20:46:04: Done! pass1 - making usageList (737 chroms): 1 millis pass2 - checking and writing primary data (3134 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:46:05: 4000000 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 20:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.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 20:46:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:46:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:46:12: 5000000 INFO @ Sun, 21 Jun 2020 20:46:14: 1000000 INFO @ Sun, 21 Jun 2020 20:46:20: 6000000 INFO @ Sun, 21 Jun 2020 20:46:21: 2000000 INFO @ Sun, 21 Jun 2020 20:46:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:46:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:46:22: #1 total tags in treatment: 6314376 INFO @ Sun, 21 Jun 2020 20:46:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:46:22: #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 20:46:22: #1 tags after filtering in treatment: 6314309 INFO @ Sun, 21 Jun 2020 20:46:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:46:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:46:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:46:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:46:23: #2 number of paired peaks: 3560 INFO @ Sun, 21 Jun 2020 20:46:23: start model_add_line... INFO @ Sun, 21 Jun 2020 20:46:23: start X-correlation... INFO @ Sun, 21 Jun 2020 20:46:23: end of X-cor INFO @ Sun, 21 Jun 2020 20:46:23: #2 finished! INFO @ Sun, 21 Jun 2020 20:46:23: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:46:23: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 20:46:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.10_model.r WARNING @ Sun, 21 Jun 2020 20:46:23: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:46:23: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 20:46:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:46:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:46:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:46:27: 3000000 INFO @ Sun, 21 Jun 2020 20:46:33: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:46:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:46:39: 5000000 INFO @ Sun, 21 Jun 2020 20:46:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:46:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:46:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.10_summits.bed INFO @ Sun, 21 Jun 2020 20:46:42: Done! pass1 - making usageList (597 chroms): 1 millis pass2 - checking and writing primary data (2330 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:46:45: 6000000 INFO @ Sun, 21 Jun 2020 20:46:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:46:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:46:47: #1 total tags in treatment: 6314376 INFO @ Sun, 21 Jun 2020 20:46:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:46:47: #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 20:46:47: #1 tags after filtering in treatment: 6314309 INFO @ Sun, 21 Jun 2020 20:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:46:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:46:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:46:48: #2 number of paired peaks: 3560 INFO @ Sun, 21 Jun 2020 20:46:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:46:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:46:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:46:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:46:48: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:46:48: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 20:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.20_model.r WARNING @ Sun, 21 Jun 2020 20:46:48: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:46:48: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 20:46:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:46:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:46:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:47:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:47:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:47:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:47:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4580643/SRX4580643.20_summits.bed INFO @ Sun, 21 Jun 2020 20:47:07: Done! pass1 - making usageList (407 chroms): 1 millis pass2 - checking and writing primary data (925 records, 4 fields): 13 millis CompletedMACS2peakCalling