Job ID = 6453121 SRX = SRX1037259 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:08:18 prefetch.2.10.7: 1) Downloading 'SRR2038537'... 2020-06-21T08:08:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:11:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:11:04 prefetch.2.10.7: 1) 'SRR2038537' was downloaded successfully Read 28586485 spots for SRR2038537/SRR2038537.sra Written 28586485 spots for SRR2038537/SRR2038537.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:47 28586485 reads; of these: 28586485 (100.00%) were unpaired; of these: 3510990 (12.28%) aligned 0 times 20595524 (72.05%) aligned exactly 1 time 4479971 (15.67%) aligned >1 times 87.72% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 17414326 / 25075495 = 0.6945 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 17:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.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 17:21:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:15: 1000000 INFO @ Sun, 21 Jun 2020 17:21:19: 2000000 INFO @ Sun, 21 Jun 2020 17:21:24: 3000000 INFO @ Sun, 21 Jun 2020 17:21:29: 4000000 INFO @ Sun, 21 Jun 2020 17:21:34: 5000000 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 17:21:39: 6000000 INFO @ Sun, 21 Jun 2020 17:21:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.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 17:21:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:44: 7000000 INFO @ Sun, 21 Jun 2020 17:21:45: 1000000 INFO @ Sun, 21 Jun 2020 17:21:48: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:21:48: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:21:48: #1 total tags in treatment: 7661169 INFO @ Sun, 21 Jun 2020 17:21:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:48: #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 17:21:48: #1 tags after filtering in treatment: 7660948 INFO @ Sun, 21 Jun 2020 17:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:49: #2 number of paired peaks: 5788 INFO @ Sun, 21 Jun 2020 17:21:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:49: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:21:49: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.05_model.r WARNING @ Sun, 21 Jun 2020 17:21:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:21:49: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:21:49: #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 17:21:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:21:50: 2000000 INFO @ Sun, 21 Jun 2020 17:21:55: 3000000 INFO @ Sun, 21 Jun 2020 17:21:59: 4000000 INFO @ Sun, 21 Jun 2020 17:22:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:22:04: 5000000 INFO @ Sun, 21 Jun 2020 17:22:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:22:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:22:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.05_summits.bed INFO @ Sun, 21 Jun 2020 17:22:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 17:22:09: 6000000 INFO @ Sun, 21 Jun 2020 17:22:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.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 17:22:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:14: 7000000 INFO @ Sun, 21 Jun 2020 17:22:15: 1000000 INFO @ Sun, 21 Jun 2020 17:22:18: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:22:18: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:22:18: #1 total tags in treatment: 7661169 INFO @ Sun, 21 Jun 2020 17:22:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:18: #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 17:22:18: #1 tags after filtering in treatment: 7660948 INFO @ Sun, 21 Jun 2020 17:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:19: #2 number of paired peaks: 5788 INFO @ Sun, 21 Jun 2020 17:22:19: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:20: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:22:20: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:22:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.10_model.r WARNING @ Sun, 21 Jun 2020 17:22:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:22:20: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:22:20: #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 17:22:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:20: 2000000 INFO @ Sun, 21 Jun 2020 17:22:25: 3000000 INFO @ Sun, 21 Jun 2020 17:22:30: 4000000 INFO @ Sun, 21 Jun 2020 17:22:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:22:35: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:22:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:22:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:22:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.10_summits.bed INFO @ Sun, 21 Jun 2020 17:22:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:22:40: 6000000 INFO @ Sun, 21 Jun 2020 17:22:45: 7000000 INFO @ Sun, 21 Jun 2020 17:22:48: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:22:48: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:22:48: #1 total tags in treatment: 7661169 INFO @ Sun, 21 Jun 2020 17:22:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:48: #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 17:22:48: #1 tags after filtering in treatment: 7660948 INFO @ Sun, 21 Jun 2020 17:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:48: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:22:49: #2 number of paired peaks: 5788 INFO @ Sun, 21 Jun 2020 17:22:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:50: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:22:50: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 17:22:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.20_model.r WARNING @ Sun, 21 Jun 2020 17:22:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:22:50: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 17:22:50: #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 17:22:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1037259/SRX1037259.20_summits.bed INFO @ Sun, 21 Jun 2020 17:23:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling