Job ID = 6454192 SRX = SRX186113 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:56:19 prefetch.2.10.7: 1) Downloading 'SRR567590'... 2020-06-21T08:56:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:59:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:59:28 prefetch.2.10.7: 1) 'SRR567590' was downloaded successfully Read 22114909 spots for SRR567590/SRR567590.sra Written 22114909 spots for SRR567590/SRR567590.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: 00:05:05 22114909 reads; of these: 22114909 (100.00%) were unpaired; of these: 4765804 (21.55%) aligned 0 times 13574478 (61.38%) aligned exactly 1 time 3774627 (17.07%) aligned >1 times 78.45% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 12132576 / 17349105 = 0.6993 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 18:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.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 18:09:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:26: 1000000 INFO @ Sun, 21 Jun 2020 18:09:31: 2000000 INFO @ Sun, 21 Jun 2020 18:09:36: 3000000 INFO @ Sun, 21 Jun 2020 18:09:41: 4000000 INFO @ Sun, 21 Jun 2020 18:09:46: 5000000 INFO @ Sun, 21 Jun 2020 18:09:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:09:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:09:47: #1 total tags in treatment: 5216529 INFO @ Sun, 21 Jun 2020 18:09:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:47: #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 18:09:48: #1 tags after filtering in treatment: 5216526 INFO @ Sun, 21 Jun 2020 18:09:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:48: #2 number of paired peaks: 1672 INFO @ Sun, 21 Jun 2020 18:09:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:48: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:09:48: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 18:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.05_model.r WARNING @ Sun, 21 Jun 2020 18:09:48: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:09:48: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 18:09:48: #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 18:09:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:48: #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 18:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.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 18:09:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:57: 1000000 INFO @ Sun, 21 Jun 2020 18:10:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:03: 2000000 INFO @ Sun, 21 Jun 2020 18:10:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.05_summits.bed INFO @ Sun, 21 Jun 2020 18:10:06: Done! pass1 - making usageList (740 chroms): 2 millis pass2 - checking and writing primary data (3495 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:10:08: 3000000 INFO @ Sun, 21 Jun 2020 18:10:14: 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 18:10:20: 5000000 INFO @ Sun, 21 Jun 2020 18:10:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:10:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:10:21: #1 total tags in treatment: 5216529 INFO @ Sun, 21 Jun 2020 18:10:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:21: #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 18:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.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 18:10:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:21: #1 tags after filtering in treatment: 5216526 INFO @ Sun, 21 Jun 2020 18:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:22: #2 number of paired peaks: 1672 INFO @ Sun, 21 Jun 2020 18:10:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:22: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:10:22: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 18:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.10_model.r WARNING @ Sun, 21 Jun 2020 18:10:22: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:10:22: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 18:10:22: #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 18:10:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:27: 1000000 INFO @ Sun, 21 Jun 2020 18:10:32: 2000000 INFO @ Sun, 21 Jun 2020 18:10:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:38: 3000000 INFO @ Sun, 21 Jun 2020 18:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.10_summits.bed INFO @ Sun, 21 Jun 2020 18:10:39: Done! pass1 - making usageList (557 chroms): 2 millis pass2 - checking and writing primary data (2146 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:10:44: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:10:50: 5000000 INFO @ Sun, 21 Jun 2020 18:10:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:10:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:10:51: #1 total tags in treatment: 5216529 INFO @ Sun, 21 Jun 2020 18:10:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:51: #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 18:10:51: #1 tags after filtering in treatment: 5216526 INFO @ Sun, 21 Jun 2020 18:10:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:52: #2 number of paired peaks: 1672 INFO @ Sun, 21 Jun 2020 18:10:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:52: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:10:52: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 18:10:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.20_model.r WARNING @ Sun, 21 Jun 2020 18:10:52: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:10:52: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sun, 21 Jun 2020 18:10:52: #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 18:10:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:11:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186113/SRX186113.20_summits.bed INFO @ Sun, 21 Jun 2020 18:11:09: Done! pass1 - making usageList (427 chroms): 1 millis pass2 - checking and writing primary data (1347 records, 4 fields): 13 millis CompletedMACS2peakCalling