Job ID = 6527764 SRX = SRX271404 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:50:14 prefetch.2.10.7: 1) Downloading 'SRR833687'... 2020-06-29T13:50:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:52:03 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:52:03 prefetch.2.10.7: 'SRR833687' is valid 2020-06-29T13:52:03 prefetch.2.10.7: 1) 'SRR833687' was downloaded successfully Read 13072688 spots for SRR833687/SRR833687.sra Written 13072688 spots for SRR833687/SRR833687.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: 00:00:01 Multiseed full-index search: 00:07:21 13072688 reads; of these: 13072688 (100.00%) were unpaired; of these: 1320546 (10.10%) aligned 0 times 5336981 (40.83%) aligned exactly 1 time 6415161 (49.07%) aligned >1 times 89.90% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3417518 / 11752142 = 0.2908 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 @ Mon, 29 Jun 2020 23:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.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 @ Mon, 29 Jun 2020 23:05:41: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:05:41: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:05:47: 1000000 INFO @ Mon, 29 Jun 2020 23:05:53: 2000000 INFO @ Mon, 29 Jun 2020 23:05:59: 3000000 INFO @ Mon, 29 Jun 2020 23:06:04: 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 @ Mon, 29 Jun 2020 23:06:10: 5000000 INFO @ Mon, 29 Jun 2020 23:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.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 @ Mon, 29 Jun 2020 23:06:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:06:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:06:16: 6000000 INFO @ Mon, 29 Jun 2020 23:06:17: 1000000 INFO @ Mon, 29 Jun 2020 23:06:22: 7000000 INFO @ Mon, 29 Jun 2020 23:06:22: 2000000 INFO @ Mon, 29 Jun 2020 23:06:27: 3000000 INFO @ Mon, 29 Jun 2020 23:06:28: 8000000 INFO @ Mon, 29 Jun 2020 23:06:30: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:06:30: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:06:30: #1 total tags in treatment: 8334624 INFO @ Mon, 29 Jun 2020 23:06:30: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:06:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:06:30: #1 tags after filtering in treatment: 8334624 INFO @ Mon, 29 Jun 2020 23:06:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:06:30: #1 finished! INFO @ Mon, 29 Jun 2020 23:06:30: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:06:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:06:31: #2 number of paired peaks: 2293 INFO @ Mon, 29 Jun 2020 23:06:31: start model_add_line... INFO @ Mon, 29 Jun 2020 23:06:31: start X-correlation... INFO @ Mon, 29 Jun 2020 23:06:31: end of X-cor INFO @ Mon, 29 Jun 2020 23:06:31: #2 finished! INFO @ Mon, 29 Jun 2020 23:06:31: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:06:31: #2 alternative fragment length(s) may be 2,11,30 bps INFO @ Mon, 29 Jun 2020 23:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.05_model.r WARNING @ Mon, 29 Jun 2020 23:06:31: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:06:31: #2 You may need to consider one of the other alternative d(s): 2,11,30 WARNING @ Mon, 29 Jun 2020 23:06:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:06:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:06:32: 4000000 INFO @ Mon, 29 Jun 2020 23:06:38: 5000000 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 @ Mon, 29 Jun 2020 23:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.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 @ Mon, 29 Jun 2020 23:06:41: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:06:41: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:06:43: 6000000 INFO @ Mon, 29 Jun 2020 23:06:47: 1000000 INFO @ Mon, 29 Jun 2020 23:06:47: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:06:48: 7000000 INFO @ Mon, 29 Jun 2020 23:06:52: 2000000 INFO @ Mon, 29 Jun 2020 23:06:53: 8000000 INFO @ Mon, 29 Jun 2020 23:06:55: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:06:55: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:06:55: #1 total tags in treatment: 8334624 INFO @ Mon, 29 Jun 2020 23:06:55: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:06:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:06:55: #1 tags after filtering in treatment: 8334624 INFO @ Mon, 29 Jun 2020 23:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:06:55: #1 finished! INFO @ Mon, 29 Jun 2020 23:06:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:06:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:06:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:06:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.05_summits.bed INFO @ Mon, 29 Jun 2020 23:06:55: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:06:56: #2 number of paired peaks: 2293 INFO @ Mon, 29 Jun 2020 23:06:56: start model_add_line... INFO @ Mon, 29 Jun 2020 23:06:56: start X-correlation... INFO @ Mon, 29 Jun 2020 23:06:56: end of X-cor INFO @ Mon, 29 Jun 2020 23:06:56: #2 finished! INFO @ Mon, 29 Jun 2020 23:06:56: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:06:56: #2 alternative fragment length(s) may be 2,11,30 bps INFO @ Mon, 29 Jun 2020 23:06:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.10_model.r WARNING @ Mon, 29 Jun 2020 23:06:56: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:06:56: #2 You may need to consider one of the other alternative d(s): 2,11,30 WARNING @ Mon, 29 Jun 2020 23:06:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:06:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:06:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:06:57: 3000000 INFO @ Mon, 29 Jun 2020 23:07:02: 4000000 INFO @ Mon, 29 Jun 2020 23:07:07: 5000000 INFO @ Mon, 29 Jun 2020 23:07:12: 6000000 INFO @ Mon, 29 Jun 2020 23:07:13: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:07:17: 7000000 INFO @ Mon, 29 Jun 2020 23:07:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:07:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:07:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.10_summits.bed INFO @ Mon, 29 Jun 2020 23:07:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:07:22: 8000000 INFO @ Mon, 29 Jun 2020 23:07:24: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:07:24: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:07:24: #1 total tags in treatment: 8334624 INFO @ Mon, 29 Jun 2020 23:07:24: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:07:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:07:24: #1 tags after filtering in treatment: 8334624 INFO @ Mon, 29 Jun 2020 23:07:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:07:24: #1 finished! INFO @ Mon, 29 Jun 2020 23:07:24: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:07:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:07:25: #2 number of paired peaks: 2293 INFO @ Mon, 29 Jun 2020 23:07:25: start model_add_line... INFO @ Mon, 29 Jun 2020 23:07:25: start X-correlation... INFO @ Mon, 29 Jun 2020 23:07:25: end of X-cor INFO @ Mon, 29 Jun 2020 23:07:25: #2 finished! INFO @ Mon, 29 Jun 2020 23:07:25: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:07:25: #2 alternative fragment length(s) may be 2,11,30 bps INFO @ Mon, 29 Jun 2020 23:07:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.20_model.r WARNING @ Mon, 29 Jun 2020 23:07:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:07:25: #2 You may need to consider one of the other alternative d(s): 2,11,30 WARNING @ Mon, 29 Jun 2020 23:07:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:07:25: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:07:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:07:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX271404/SRX271404.20_summits.bed INFO @ Mon, 29 Jun 2020 23:07:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling