Job ID = 6454770 SRX = SRX2583183 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:39:40 prefetch.2.10.7: 1) Downloading 'SRR5279383'... 2020-06-21T09:39:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:08 prefetch.2.10.7: 'SRR5279383' is valid 2020-06-21T09:41:08 prefetch.2.10.7: 1) 'SRR5279383' was downloaded successfully 2020-06-21T09:41:08 prefetch.2.10.7: 'SRR5279383' has 0 unresolved dependencies Read 12461600 spots for SRR5279383/SRR5279383.sra Written 12461600 spots for SRR5279383/SRR5279383.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: 00:03:38 12461600 reads; of these: 12461600 (100.00%) were unpaired; of these: 1846550 (14.82%) aligned 0 times 7446024 (59.75%) aligned exactly 1 time 3169026 (25.43%) aligned >1 times 85.18% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5871312 / 10615050 = 0.5531 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 18:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.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 18:48:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:41: 1000000 INFO @ Sun, 21 Jun 2020 18:48:47: 2000000 INFO @ Sun, 21 Jun 2020 18:48:53: 3000000 INFO @ Sun, 21 Jun 2020 18:49:00: 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 18:49:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:04: #1 total tags in treatment: 4743738 INFO @ Sun, 21 Jun 2020 18:49:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:04: #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 18:49:05: #1 tags after filtering in treatment: 4743597 INFO @ Sun, 21 Jun 2020 18:49:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:05: #2 number of paired peaks: 2467 INFO @ Sun, 21 Jun 2020 18:49:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:05: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 18:49:05: #2 alternative fragment length(s) may be 92,574 bps INFO @ Sun, 21 Jun 2020 18:49:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.05_model.r WARNING @ Sun, 21 Jun 2020 18:49:05: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:05: #2 You may need to consider one of the other alternative d(s): 92,574 WARNING @ Sun, 21 Jun 2020 18:49:05: #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 18:49:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.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 18:49:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:13: 1000000 INFO @ Sun, 21 Jun 2020 18:49:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:19: 2000000 INFO @ Sun, 21 Jun 2020 18:49:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.05_summits.bed INFO @ Sun, 21 Jun 2020 18:49:23: Done! pass1 - making usageList (705 chroms): 1 millis pass2 - checking and writing primary data (2795 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:25: 3000000 INFO @ Sun, 21 Jun 2020 18:49:32: 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 18:49:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.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 18:49:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:37: #1 total tags in treatment: 4743738 INFO @ Sun, 21 Jun 2020 18:49:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:37: #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 18:49:37: #1 tags after filtering in treatment: 4743597 INFO @ Sun, 21 Jun 2020 18:49:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:37: #2 number of paired peaks: 2467 INFO @ Sun, 21 Jun 2020 18:49:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:37: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 18:49:37: #2 alternative fragment length(s) may be 92,574 bps INFO @ Sun, 21 Jun 2020 18:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.10_model.r WARNING @ Sun, 21 Jun 2020 18:49:37: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:37: #2 You may need to consider one of the other alternative d(s): 92,574 WARNING @ Sun, 21 Jun 2020 18:49:37: #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 18:49:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:41: 1000000 INFO @ Sun, 21 Jun 2020 18:49:47: 2000000 INFO @ Sun, 21 Jun 2020 18:49:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:54: 3000000 INFO @ Sun, 21 Jun 2020 18:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.10_summits.bed INFO @ Sun, 21 Jun 2020 18:49:55: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (1454 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:00: 4000000 INFO @ Sun, 21 Jun 2020 18:50:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:50:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:50:05: #1 total tags in treatment: 4743738 INFO @ Sun, 21 Jun 2020 18:50:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:05: #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 18:50:05: #1 tags after filtering in treatment: 4743597 INFO @ Sun, 21 Jun 2020 18:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:06: #2 number of paired peaks: 2467 INFO @ Sun, 21 Jun 2020 18:50:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:06: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 18:50:06: #2 alternative fragment length(s) may be 92,574 bps INFO @ Sun, 21 Jun 2020 18:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.20_model.r WARNING @ Sun, 21 Jun 2020 18:50:06: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:06: #2 You may need to consider one of the other alternative d(s): 92,574 WARNING @ Sun, 21 Jun 2020 18:50:06: #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 18:50:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:50:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583183/SRX2583183.20_summits.bed INFO @ Sun, 21 Jun 2020 18:50:23: Done! pass1 - making usageList (216 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 7 millis CompletedMACS2peakCalling