Job ID = 6455139 SRX = SRX2788640 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:55 prefetch.2.10.7: 1) Downloading 'SRR5515260'... 2020-06-21T09:53:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:06:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:06:27 prefetch.2.10.7: 1) 'SRR5515260' was downloaded successfully 2020-06-21T10:06:28 prefetch.2.10.7: 'SRR5515260' has 0 unresolved dependencies Read 51690992 spots for SRR5515260/SRR5515260.sra Written 51690992 spots for SRR5515260/SRR5515260.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: 00:15:30 51690992 reads; of these: 51690992 (100.00%) were unpaired; of these: 18226045 (35.26%) aligned 0 times 28897623 (55.90%) aligned exactly 1 time 4567324 (8.84%) aligned >1 times 64.74% overall alignment rate Time searching: 00:15:30 Overall time: 00:15:30 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 16 files... [bam_rmdupse_core] 30569871 / 33464947 = 0.9135 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 19:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.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 19:35:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:11: 1000000 INFO @ Sun, 21 Jun 2020 19:35:18: 2000000 INFO @ Sun, 21 Jun 2020 19:35:26: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 19:35:26: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 19:35:26: #1 total tags in treatment: 2895076 INFO @ Sun, 21 Jun 2020 19:35:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:26: #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 19:35:26: #1 tags after filtering in treatment: 2894909 INFO @ Sun, 21 Jun 2020 19:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:26: #2 number of paired peaks: 4088 INFO @ Sun, 21 Jun 2020 19:35:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:26: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 19:35:26: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 19:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.05_model.r WARNING @ Sun, 21 Jun 2020 19:35:26: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:26: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 21 Jun 2020 19:35:26: #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 19:35:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:26: #3 Pre-compute pvalue-qvalue table... 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 19:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.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 19:35:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.05_summits.bed INFO @ Sun, 21 Jun 2020 19:35:37: Done! pass1 - making usageList (646 chroms): 1 millis pass2 - checking and writing primary data (2740 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:43: 1000000 INFO @ Sun, 21 Jun 2020 19:35:53: 2000000 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 19:36:02: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 19:36:02: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 19:36:02: #1 total tags in treatment: 2895076 INFO @ Sun, 21 Jun 2020 19:36:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:02: #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 19:36:02: #1 tags after filtering in treatment: 2894909 INFO @ Sun, 21 Jun 2020 19:36:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:02: #2 number of paired peaks: 4088 INFO @ Sun, 21 Jun 2020 19:36:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:02: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 19:36:02: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 19:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.10_model.r WARNING @ Sun, 21 Jun 2020 19:36:02: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:02: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 21 Jun 2020 19:36:02: #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 19:36:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.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 19:36:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:13: 1000000 INFO @ Sun, 21 Jun 2020 19:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.10_summits.bed INFO @ Sun, 21 Jun 2020 19:36:13: Done! pass1 - making usageList (426 chroms): 1 millis pass2 - checking and writing primary data (1033 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:22: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:36:31: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 19:36:31: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 19:36:31: #1 total tags in treatment: 2895076 INFO @ Sun, 21 Jun 2020 19:36:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:31: #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 19:36:31: #1 tags after filtering in treatment: 2894909 INFO @ Sun, 21 Jun 2020 19:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:31: #2 number of paired peaks: 4088 INFO @ Sun, 21 Jun 2020 19:36:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:31: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 19:36:31: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 21 Jun 2020 19:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.20_model.r WARNING @ Sun, 21 Jun 2020 19:36:31: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:31: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 21 Jun 2020 19:36:31: #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 19:36:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788640/SRX2788640.20_summits.bed INFO @ Sun, 21 Jun 2020 19:36:42: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (337 records, 4 fields): 7 millis CompletedMACS2peakCalling