Job ID = 6458620 SRX = SRX5343151 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:32:49 prefetch.2.10.7: 1) Downloading 'SRR8540851'... 2020-06-21T12:32:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:23 prefetch.2.10.7: 1) 'SRR8540851' was downloaded successfully 2020-06-21T12:35:23 prefetch.2.10.7: 'SRR8540851' has 0 unresolved dependencies Read 20780672 spots for SRR8540851/SRR8540851.sra Written 20780672 spots for SRR8540851/SRR8540851.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: 00:05:57 20780672 reads; of these: 20780672 (100.00%) were unpaired; of these: 3687597 (17.75%) aligned 0 times 12517046 (60.23%) aligned exactly 1 time 4576029 (22.02%) aligned >1 times 82.25% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 7417521 / 17093075 = 0.4339 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 21:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.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 21:46:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:59: 1000000 INFO @ Sun, 21 Jun 2020 21:47:04: 2000000 INFO @ Sun, 21 Jun 2020 21:47:10: 3000000 INFO @ Sun, 21 Jun 2020 21:47:16: 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 21:47:22: 5000000 INFO @ Sun, 21 Jun 2020 21:47:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.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 21:47:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:47:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:28: 6000000 INFO @ Sun, 21 Jun 2020 21:47:31: 1000000 INFO @ Sun, 21 Jun 2020 21:47:35: 7000000 INFO @ Sun, 21 Jun 2020 21:47:38: 2000000 INFO @ Sun, 21 Jun 2020 21:47:43: 8000000 INFO @ Sun, 21 Jun 2020 21:47:46: 3000000 INFO @ Sun, 21 Jun 2020 21:47:50: 9000000 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 21:47:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.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 21:47:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:47:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:54: 4000000 INFO @ Sun, 21 Jun 2020 21:47:55: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:47:55: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:47:55: #1 total tags in treatment: 9675554 INFO @ Sun, 21 Jun 2020 21:47:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:55: #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 21:47:55: #1 tags after filtering in treatment: 9675553 INFO @ Sun, 21 Jun 2020 21:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:56: #2 number of paired peaks: 1446 INFO @ Sun, 21 Jun 2020 21:47:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:56: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:47:56: #2 alternative fragment length(s) may be 4,91,102,598 bps INFO @ Sun, 21 Jun 2020 21:47:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.05_model.r WARNING @ Sun, 21 Jun 2020 21:47:56: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:56: #2 You may need to consider one of the other alternative d(s): 4,91,102,598 WARNING @ Sun, 21 Jun 2020 21:47:56: #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 21:47:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:01: 1000000 INFO @ Sun, 21 Jun 2020 21:48:01: 5000000 INFO @ Sun, 21 Jun 2020 21:48:08: 2000000 INFO @ Sun, 21 Jun 2020 21:48:09: 6000000 INFO @ Sun, 21 Jun 2020 21:48:16: 3000000 INFO @ Sun, 21 Jun 2020 21:48:16: 7000000 INFO @ Sun, 21 Jun 2020 21:48:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:23: 4000000 INFO @ Sun, 21 Jun 2020 21:48:24: 8000000 INFO @ Sun, 21 Jun 2020 21:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.05_summits.bed INFO @ Sun, 21 Jun 2020 21:48:27: Done! pass1 - making usageList (696 chroms): 1 millis pass2 - checking and writing primary data (2262 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:48:31: 5000000 INFO @ Sun, 21 Jun 2020 21:48:32: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:48:37: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:48:37: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:48:37: #1 total tags in treatment: 9675554 INFO @ Sun, 21 Jun 2020 21:48:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:37: #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 21:48:38: #1 tags after filtering in treatment: 9675553 INFO @ Sun, 21 Jun 2020 21:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:38: #2 number of paired peaks: 1446 INFO @ Sun, 21 Jun 2020 21:48:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:38: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:48:38: #2 alternative fragment length(s) may be 4,91,102,598 bps INFO @ Sun, 21 Jun 2020 21:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.10_model.r WARNING @ Sun, 21 Jun 2020 21:48:38: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:48:38: #2 You may need to consider one of the other alternative d(s): 4,91,102,598 WARNING @ Sun, 21 Jun 2020 21:48:38: #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 21:48:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:39: 6000000 INFO @ Sun, 21 Jun 2020 21:48:46: 7000000 INFO @ Sun, 21 Jun 2020 21:48:53: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:48:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:49:01: 9000000 INFO @ Sun, 21 Jun 2020 21:49:05: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:49:05: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:49:05: #1 total tags in treatment: 9675554 INFO @ Sun, 21 Jun 2020 21:49:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:49:05: #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 21:49:06: #1 tags after filtering in treatment: 9675553 INFO @ Sun, 21 Jun 2020 21:49:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:49:06: #1 finished! INFO @ Sun, 21 Jun 2020 21:49:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:49:07: #2 number of paired peaks: 1446 INFO @ Sun, 21 Jun 2020 21:49:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:49:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:49:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:49:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:49:07: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:49:07: #2 alternative fragment length(s) may be 4,91,102,598 bps INFO @ Sun, 21 Jun 2020 21:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.20_model.r WARNING @ Sun, 21 Jun 2020 21:49:07: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:49:07: #2 You may need to consider one of the other alternative d(s): 4,91,102,598 WARNING @ Sun, 21 Jun 2020 21:49:07: #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 21:49:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.10_summits.bed INFO @ Sun, 21 Jun 2020 21:49:09: Done! pass1 - making usageList (408 chroms): 1 millis pass2 - checking and writing primary data (929 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:49:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343151/SRX5343151.20_summits.bed INFO @ Sun, 21 Jun 2020 21:49:35: Done! pass1 - making usageList (204 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 7 millis CompletedMACS2peakCalling