Job ID = 6459074 SRX = SRX6386751 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:58:35 prefetch.2.10.7: 1) Downloading 'SRR9624483'... 2020-06-21T12:58:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:06:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:06:03 prefetch.2.10.7: 1) 'SRR9624483' was downloaded successfully Read 29923810 spots for SRR9624483/SRR9624483.sra Written 29923810 spots for SRR9624483/SRR9624483.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: 00:06:50 29923810 reads; of these: 29923810 (100.00%) were unpaired; of these: 8129588 (27.17%) aligned 0 times 15926395 (53.22%) aligned exactly 1 time 5867827 (19.61%) aligned >1 times 72.83% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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 12 files... [bam_rmdupse_core] 12998540 / 21794222 = 0.5964 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 22:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.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 22:18:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:57: 1000000 INFO @ Sun, 21 Jun 2020 22:19:05: 2000000 INFO @ Sun, 21 Jun 2020 22:19:12: 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 22:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.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 22:19:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:20: 4000000 INFO @ Sun, 21 Jun 2020 22:19:27: 1000000 INFO @ Sun, 21 Jun 2020 22:19:29: 5000000 INFO @ Sun, 21 Jun 2020 22:19:35: 2000000 INFO @ Sun, 21 Jun 2020 22:19:37: 6000000 INFO @ Sun, 21 Jun 2020 22:19:43: 3000000 INFO @ Sun, 21 Jun 2020 22:19:46: 7000000 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 22:19:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.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 22:19:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:50: 4000000 INFO @ Sun, 21 Jun 2020 22:19:55: 8000000 INFO @ Sun, 21 Jun 2020 22:19:57: 1000000 INFO @ Sun, 21 Jun 2020 22:19:58: 5000000 INFO @ Sun, 21 Jun 2020 22:20:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:20:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:20:01: #1 total tags in treatment: 8795682 INFO @ Sun, 21 Jun 2020 22:20:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:20:01: #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 22:20:02: #1 tags after filtering in treatment: 8795670 INFO @ Sun, 21 Jun 2020 22:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:20:02: #1 finished! INFO @ Sun, 21 Jun 2020 22:20:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:20:03: #2 number of paired peaks: 1597 INFO @ Sun, 21 Jun 2020 22:20:03: start model_add_line... INFO @ Sun, 21 Jun 2020 22:20:03: start X-correlation... INFO @ Sun, 21 Jun 2020 22:20:03: end of X-cor INFO @ Sun, 21 Jun 2020 22:20:03: #2 finished! INFO @ Sun, 21 Jun 2020 22:20:03: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:20:03: #2 alternative fragment length(s) may be 3,48,564 bps INFO @ Sun, 21 Jun 2020 22:20:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.05_model.r WARNING @ Sun, 21 Jun 2020 22:20:03: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:20:03: #2 You may need to consider one of the other alternative d(s): 3,48,564 WARNING @ Sun, 21 Jun 2020 22:20:03: #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 22:20:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:20:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:20:05: 2000000 INFO @ Sun, 21 Jun 2020 22:20:06: 6000000 INFO @ Sun, 21 Jun 2020 22:20:12: 3000000 INFO @ Sun, 21 Jun 2020 22:20:14: 7000000 INFO @ Sun, 21 Jun 2020 22:20:20: 4000000 INFO @ Sun, 21 Jun 2020 22:20:21: 8000000 INFO @ Sun, 21 Jun 2020 22:20:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:20:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:20:27: #1 total tags in treatment: 8795682 INFO @ Sun, 21 Jun 2020 22:20:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:20:27: #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 22:20:27: 5000000 INFO @ Sun, 21 Jun 2020 22:20:27: #1 tags after filtering in treatment: 8795670 INFO @ Sun, 21 Jun 2020 22:20:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:20:27: #1 finished! INFO @ Sun, 21 Jun 2020 22:20:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:20:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:20:28: #2 number of paired peaks: 1597 INFO @ Sun, 21 Jun 2020 22:20:28: start model_add_line... INFO @ Sun, 21 Jun 2020 22:20:28: start X-correlation... INFO @ Sun, 21 Jun 2020 22:20:28: end of X-cor INFO @ Sun, 21 Jun 2020 22:20:28: #2 finished! INFO @ Sun, 21 Jun 2020 22:20:28: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:20:28: #2 alternative fragment length(s) may be 3,48,564 bps INFO @ Sun, 21 Jun 2020 22:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.10_model.r WARNING @ Sun, 21 Jun 2020 22:20:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:20:28: #2 You may need to consider one of the other alternative d(s): 3,48,564 WARNING @ Sun, 21 Jun 2020 22:20:28: #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 22:20:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:20:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.05_summits.bed INFO @ Sun, 21 Jun 2020 22:20:30: Done! pass1 - making usageList (724 chroms): 1 millis pass2 - checking and writing primary data (3003 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:20:34: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:20:41: 7000000 INFO @ Sun, 21 Jun 2020 22:20:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:48: 8000000 INFO @ Sun, 21 Jun 2020 22:20:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:20:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:20:53: #1 total tags in treatment: 8795682 INFO @ Sun, 21 Jun 2020 22:20:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:20:53: #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 22:20:53: #1 tags after filtering in treatment: 8795670 INFO @ Sun, 21 Jun 2020 22:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:20:53: #1 finished! INFO @ Sun, 21 Jun 2020 22:20:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:20:54: #2 number of paired peaks: 1597 INFO @ Sun, 21 Jun 2020 22:20:54: start model_add_line... INFO @ Sun, 21 Jun 2020 22:20:54: start X-correlation... INFO @ Sun, 21 Jun 2020 22:20:54: end of X-cor INFO @ Sun, 21 Jun 2020 22:20:54: #2 finished! INFO @ Sun, 21 Jun 2020 22:20:54: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:20:54: #2 alternative fragment length(s) may be 3,48,564 bps INFO @ Sun, 21 Jun 2020 22:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.20_model.r WARNING @ Sun, 21 Jun 2020 22:20:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:20:54: #2 You may need to consider one of the other alternative d(s): 3,48,564 WARNING @ Sun, 21 Jun 2020 22:20:54: #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 22:20:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:20:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.10_summits.bed INFO @ Sun, 21 Jun 2020 22:20:56: Done! pass1 - making usageList (590 chroms): 1 millis pass2 - checking and writing primary data (2377 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:21:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:21:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:21:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:21:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386751/SRX6386751.20_summits.bed INFO @ Sun, 21 Jun 2020 22:21:22: Done! pass1 - making usageList (508 chroms): 2 millis pass2 - checking and writing primary data (1632 records, 4 fields): 16 millis CompletedMACS2peakCalling