Job ID = 6458392 SRX = SRX511132 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:22:24 prefetch.2.10.7: 1) Downloading 'SRR1217237'... 2020-06-21T12:22:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:23:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:23:29 prefetch.2.10.7: 'SRR1217237' is valid 2020-06-21T12:23:29 prefetch.2.10.7: 1) 'SRR1217237' was downloaded successfully Read 9255352 spots for SRR1217237/SRR1217237.sra Written 9255352 spots for SRR1217237/SRR1217237.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: 00:03:09 9255352 reads; of these: 9255352 (100.00%) were unpaired; of these: 236834 (2.56%) aligned 0 times 5773916 (62.38%) aligned exactly 1 time 3244602 (35.06%) aligned >1 times 97.44% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 1018789 / 9018518 = 0.1130 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 21:30:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.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 21:30:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:43: 1000000 INFO @ Sun, 21 Jun 2020 21:30:50: 2000000 INFO @ Sun, 21 Jun 2020 21:30:56: 3000000 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 21:31:03: 4000000 INFO @ Sun, 21 Jun 2020 21:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.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 21:31:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:10: 5000000 INFO @ Sun, 21 Jun 2020 21:31:14: 1000000 INFO @ Sun, 21 Jun 2020 21:31:17: 6000000 INFO @ Sun, 21 Jun 2020 21:31:22: 2000000 INFO @ Sun, 21 Jun 2020 21:31:25: 7000000 INFO @ Sun, 21 Jun 2020 21:31:30: 3000000 INFO @ Sun, 21 Jun 2020 21:31:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:31:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:31:32: #1 total tags in treatment: 7999729 INFO @ Sun, 21 Jun 2020 21:31:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:31:32: #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 21:31:33: #1 tags after filtering in treatment: 7999626 INFO @ Sun, 21 Jun 2020 21:31:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:31:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:31:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:31:33: #2 looking for paired plus/minus strand peaks... 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 21:31:33: #2 number of paired peaks: 2457 INFO @ Sun, 21 Jun 2020 21:31:33: start model_add_line... INFO @ Sun, 21 Jun 2020 21:31:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:31:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:31:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:31:34: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 21:31:34: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sun, 21 Jun 2020 21:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.05_model.r WARNING @ Sun, 21 Jun 2020 21:31:34: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:31:34: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sun, 21 Jun 2020 21:31:34: #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 21:31:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:31:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.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 21:31:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:31:38: 4000000 INFO @ Sun, 21 Jun 2020 21:31:43: 1000000 INFO @ Sun, 21 Jun 2020 21:31:46: 5000000 INFO @ Sun, 21 Jun 2020 21:31:49: 2000000 INFO @ Sun, 21 Jun 2020 21:31:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:54: 6000000 INFO @ Sun, 21 Jun 2020 21:31:56: 3000000 INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.05_summits.bed INFO @ Sun, 21 Jun 2020 21:31:58: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (2614 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:32:03: 7000000 INFO @ Sun, 21 Jun 2020 21:32:03: 4000000 INFO @ Sun, 21 Jun 2020 21:32:10: 5000000 INFO @ Sun, 21 Jun 2020 21:32:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:11: #1 total tags in treatment: 7999729 INFO @ Sun, 21 Jun 2020 21:32:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:11: #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 21:32:11: #1 tags after filtering in treatment: 7999626 INFO @ Sun, 21 Jun 2020 21:32:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:12: #2 number of paired peaks: 2457 INFO @ Sun, 21 Jun 2020 21:32:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:12: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 21:32:12: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sun, 21 Jun 2020 21:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.10_model.r WARNING @ Sun, 21 Jun 2020 21:32:12: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:12: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sun, 21 Jun 2020 21:32:12: #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 21:32:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:17: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:32:25: 7000000 INFO @ Sun, 21 Jun 2020 21:32:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:32: #1 total tags in treatment: 7999729 INFO @ Sun, 21 Jun 2020 21:32:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:32: #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 21:32:33: #1 tags after filtering in treatment: 7999626 INFO @ Sun, 21 Jun 2020 21:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:32:34: #2 number of paired peaks: 2457 INFO @ Sun, 21 Jun 2020 21:32:34: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:34: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 21:32:34: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sun, 21 Jun 2020 21:32:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.20_model.r WARNING @ Sun, 21 Jun 2020 21:32:34: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:34: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sun, 21 Jun 2020 21:32:34: #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 21:32:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.10_summits.bed INFO @ Sun, 21 Jun 2020 21:32:37: Done! pass1 - making usageList (476 chroms): 1 millis pass2 - checking and writing primary data (1768 records, 4 fields): 29 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:32:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:32:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511132/SRX511132.20_summits.bed INFO @ Sun, 21 Jun 2020 21:32:58: Done! pass1 - making usageList (298 chroms): 2 millis pass2 - checking and writing primary data (630 records, 4 fields): 17 millis CompletedMACS2peakCalling