Job ID = 6508858 SRX = SRX495231 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:40:18 prefetch.2.10.7: 1) Downloading 'SRR1198736'... 2020-06-26T14:40:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:41:40 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:41:41 prefetch.2.10.7: 'SRR1198736' is valid 2020-06-26T14:41:41 prefetch.2.10.7: 1) 'SRR1198736' was downloaded successfully Read 17988834 spots for SRR1198736/SRR1198736.sra Written 17988834 spots for SRR1198736/SRR1198736.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:29 17988834 reads; of these: 17988834 (100.00%) were unpaired; of these: 4192571 (23.31%) aligned 0 times 12301338 (68.38%) aligned exactly 1 time 1494925 (8.31%) aligned >1 times 76.69% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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] 3863235 / 13796263 = 0.2800 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 @ Fri, 26 Jun 2020 23:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.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 @ Fri, 26 Jun 2020 23:49:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:49:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:49:53: 1000000 INFO @ Fri, 26 Jun 2020 23:49:59: 2000000 INFO @ Fri, 26 Jun 2020 23:50:05: 3000000 INFO @ Fri, 26 Jun 2020 23:50:11: 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 @ Fri, 26 Jun 2020 23:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.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 @ Fri, 26 Jun 2020 23:50:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:50:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:50:17: 5000000 INFO @ Fri, 26 Jun 2020 23:50:23: 1000000 INFO @ Fri, 26 Jun 2020 23:50:23: 6000000 INFO @ Fri, 26 Jun 2020 23:50:29: 7000000 INFO @ Fri, 26 Jun 2020 23:50:30: 2000000 INFO @ Fri, 26 Jun 2020 23:50:36: 8000000 INFO @ Fri, 26 Jun 2020 23:50:36: 3000000 INFO @ Fri, 26 Jun 2020 23:50:42: 4000000 INFO @ Fri, 26 Jun 2020 23:50:43: 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 @ Fri, 26 Jun 2020 23:50:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.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 @ Fri, 26 Jun 2020 23:50:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:50:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:50:49: 5000000 INFO @ Fri, 26 Jun 2020 23:50:49: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 23:50:49: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 23:50:49: #1 total tags in treatment: 9933028 INFO @ Fri, 26 Jun 2020 23:50:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:50:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:50:49: #1 tags after filtering in treatment: 9932986 INFO @ Fri, 26 Jun 2020 23:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:50:49: #1 finished! INFO @ Fri, 26 Jun 2020 23:50:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:50:50: #2 number of paired peaks: 1372 INFO @ Fri, 26 Jun 2020 23:50:50: start model_add_line... INFO @ Fri, 26 Jun 2020 23:50:50: start X-correlation... INFO @ Fri, 26 Jun 2020 23:50:50: end of X-cor INFO @ Fri, 26 Jun 2020 23:50:50: #2 finished! INFO @ Fri, 26 Jun 2020 23:50:50: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 23:50:50: #2 alternative fragment length(s) may be 3 bps INFO @ Fri, 26 Jun 2020 23:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.05_model.r WARNING @ Fri, 26 Jun 2020 23:50:50: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:50:50: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Fri, 26 Jun 2020 23:50:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:50:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:50:53: 1000000 INFO @ Fri, 26 Jun 2020 23:50:55: 6000000 INFO @ Fri, 26 Jun 2020 23:51:00: 2000000 INFO @ Fri, 26 Jun 2020 23:51:02: 7000000 INFO @ Fri, 26 Jun 2020 23:51:06: 3000000 INFO @ Fri, 26 Jun 2020 23:51:08: 8000000 INFO @ Fri, 26 Jun 2020 23:51:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:51:13: 4000000 INFO @ Fri, 26 Jun 2020 23:51:15: 9000000 INFO @ Fri, 26 Jun 2020 23:51:20: 5000000 INFO @ Fri, 26 Jun 2020 23:51:21: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 23:51:21: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 23:51:21: #1 total tags in treatment: 9933028 INFO @ Fri, 26 Jun 2020 23:51:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:51:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:51:22: #1 tags after filtering in treatment: 9932986 INFO @ Fri, 26 Jun 2020 23:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:51:22: #1 finished! INFO @ Fri, 26 Jun 2020 23:51:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:51:23: #2 number of paired peaks: 1372 INFO @ Fri, 26 Jun 2020 23:51:23: start model_add_line... INFO @ Fri, 26 Jun 2020 23:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.05_summits.bed INFO @ Fri, 26 Jun 2020 23:51:23: Done! INFO @ Fri, 26 Jun 2020 23:51:23: start X-correlation... INFO @ Fri, 26 Jun 2020 23:51:23: end of X-cor INFO @ Fri, 26 Jun 2020 23:51:23: #2 finished! INFO @ Fri, 26 Jun 2020 23:51:23: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 23:51:23: #2 alternative fragment length(s) may be 3 bps INFO @ Fri, 26 Jun 2020 23:51:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.10_model.r WARNING @ Fri, 26 Jun 2020 23:51:23: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:51:23: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Fri, 26 Jun 2020 23:51:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:51:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:51:23: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:51:26: 6000000 INFO @ Fri, 26 Jun 2020 23:51:32: 7000000 INFO @ Fri, 26 Jun 2020 23:51:38: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:51:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:51:45: 9000000 INFO @ Fri, 26 Jun 2020 23:51:50: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 23:51:50: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 23:51:50: #1 total tags in treatment: 9933028 INFO @ Fri, 26 Jun 2020 23:51:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:51:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:51:51: #1 tags after filtering in treatment: 9932986 INFO @ Fri, 26 Jun 2020 23:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:51:51: #1 finished! INFO @ Fri, 26 Jun 2020 23:51:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:51:52: #2 number of paired peaks: 1372 INFO @ Fri, 26 Jun 2020 23:51:52: start model_add_line... INFO @ Fri, 26 Jun 2020 23:51:52: start X-correlation... INFO @ Fri, 26 Jun 2020 23:51:52: end of X-cor INFO @ Fri, 26 Jun 2020 23:51:52: #2 finished! INFO @ Fri, 26 Jun 2020 23:51:52: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 23:51:52: #2 alternative fragment length(s) may be 3 bps INFO @ Fri, 26 Jun 2020 23:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.20_model.r WARNING @ Fri, 26 Jun 2020 23:51:52: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:51:52: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Fri, 26 Jun 2020 23:51:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:51:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.10_summits.bed INFO @ Fri, 26 Jun 2020 23:51:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:52:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495231/SRX495231.20_summits.bed INFO @ Fri, 26 Jun 2020 23:52:24: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling