Job ID = 6508890 SRX = SRX495285 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:28:52 prefetch.2.10.7: 1) Downloading 'SRR1198790'... 2020-06-26T15:28:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:30:11 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:30:12 prefetch.2.10.7: 'SRR1198790' is valid 2020-06-26T15:30:12 prefetch.2.10.7: 1) 'SRR1198790' was downloaded successfully Read 13102053 spots for SRR1198790/SRR1198790.sra Written 13102053 spots for SRR1198790/SRR1198790.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: 00:03:15 13102053 reads; of these: 13102053 (100.00%) were unpaired; of these: 384487 (2.93%) aligned 0 times 11047224 (84.32%) aligned exactly 1 time 1670342 (12.75%) aligned >1 times 97.07% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 4830949 / 12717566 = 0.3799 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 @ Sat, 27 Jun 2020 00:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.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 @ Sat, 27 Jun 2020 00:37:29: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:37:29: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:37:35: 1000000 INFO @ Sat, 27 Jun 2020 00:37:42: 2000000 INFO @ Sat, 27 Jun 2020 00:37:48: 3000000 INFO @ Sat, 27 Jun 2020 00:37:54: 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 @ Sat, 27 Jun 2020 00:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.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 @ Sat, 27 Jun 2020 00:37:59: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:37:59: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:38:01: 5000000 INFO @ Sat, 27 Jun 2020 00:38:05: 1000000 INFO @ Sat, 27 Jun 2020 00:38:07: 6000000 INFO @ Sat, 27 Jun 2020 00:38:12: 2000000 INFO @ Sat, 27 Jun 2020 00:38:14: 7000000 INFO @ Sat, 27 Jun 2020 00:38:18: 3000000 INFO @ Sat, 27 Jun 2020 00:38:20: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:38:20: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:38:20: #1 total tags in treatment: 7886617 INFO @ Sat, 27 Jun 2020 00:38:20: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:38:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:38:21: #1 tags after filtering in treatment: 7886496 INFO @ Sat, 27 Jun 2020 00:38:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:38:21: #1 finished! INFO @ Sat, 27 Jun 2020 00:38:21: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:38:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:38:22: #2 number of paired peaks: 6794 INFO @ Sat, 27 Jun 2020 00:38:22: start model_add_line... INFO @ Sat, 27 Jun 2020 00:38:22: start X-correlation... INFO @ Sat, 27 Jun 2020 00:38:22: end of X-cor INFO @ Sat, 27 Jun 2020 00:38:22: #2 finished! INFO @ Sat, 27 Jun 2020 00:38:22: #2 predicted fragment length is 3 bps INFO @ Sat, 27 Jun 2020 00:38:22: #2 alternative fragment length(s) may be 3,11 bps INFO @ Sat, 27 Jun 2020 00:38:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.05_model.r WARNING @ Sat, 27 Jun 2020 00:38:22: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:38:22: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Sat, 27 Jun 2020 00:38:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:38:22: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:38:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:38:25: 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 @ Sat, 27 Jun 2020 00:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.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 @ Sat, 27 Jun 2020 00:38:29: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:38:29: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:38:31: 5000000 INFO @ Sat, 27 Jun 2020 00:38:35: 1000000 INFO @ Sat, 27 Jun 2020 00:38:37: 6000000 INFO @ Sat, 27 Jun 2020 00:38:38: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:38:42: 2000000 INFO @ Sat, 27 Jun 2020 00:38:44: 7000000 INFO @ Sat, 27 Jun 2020 00:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:38:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:38:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.05_summits.bed INFO @ Sat, 27 Jun 2020 00:38:46: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:38:48: 3000000 INFO @ Sat, 27 Jun 2020 00:38:50: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:38:50: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:38:50: #1 total tags in treatment: 7886617 INFO @ Sat, 27 Jun 2020 00:38:50: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:38:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:38:51: #1 tags after filtering in treatment: 7886496 INFO @ Sat, 27 Jun 2020 00:38:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:38:51: #1 finished! INFO @ Sat, 27 Jun 2020 00:38:51: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:38:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:38:52: #2 number of paired peaks: 6794 INFO @ Sat, 27 Jun 2020 00:38:52: start model_add_line... INFO @ Sat, 27 Jun 2020 00:38:52: start X-correlation... INFO @ Sat, 27 Jun 2020 00:38:52: end of X-cor INFO @ Sat, 27 Jun 2020 00:38:52: #2 finished! INFO @ Sat, 27 Jun 2020 00:38:52: #2 predicted fragment length is 3 bps INFO @ Sat, 27 Jun 2020 00:38:52: #2 alternative fragment length(s) may be 3,11 bps INFO @ Sat, 27 Jun 2020 00:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.10_model.r WARNING @ Sat, 27 Jun 2020 00:38:52: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:38:52: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Sat, 27 Jun 2020 00:38:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:38:52: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:38:54: 4000000 INFO @ Sat, 27 Jun 2020 00:39:01: 5000000 INFO @ Sat, 27 Jun 2020 00:39:07: 6000000 INFO @ Sat, 27 Jun 2020 00:39:08: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:39:13: 7000000 INFO @ Sat, 27 Jun 2020 00:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.10_summits.bed INFO @ Sat, 27 Jun 2020 00:39:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:39:19: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:39:19: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:39:19: #1 total tags in treatment: 7886617 INFO @ Sat, 27 Jun 2020 00:39:19: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:39:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:39:19: #1 tags after filtering in treatment: 7886496 INFO @ Sat, 27 Jun 2020 00:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:39:19: #1 finished! INFO @ Sat, 27 Jun 2020 00:39:19: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:39:20: #2 number of paired peaks: 6794 INFO @ Sat, 27 Jun 2020 00:39:20: start model_add_line... INFO @ Sat, 27 Jun 2020 00:39:20: start X-correlation... INFO @ Sat, 27 Jun 2020 00:39:20: end of X-cor INFO @ Sat, 27 Jun 2020 00:39:20: #2 finished! INFO @ Sat, 27 Jun 2020 00:39:20: #2 predicted fragment length is 3 bps INFO @ Sat, 27 Jun 2020 00:39:20: #2 alternative fragment length(s) may be 3,11 bps INFO @ Sat, 27 Jun 2020 00:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.20_model.r WARNING @ Sat, 27 Jun 2020 00:39:20: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:39:20: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Sat, 27 Jun 2020 00:39:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:39:20: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:39:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:39:37: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:39:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:39:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495285/SRX495285.20_summits.bed INFO @ Sat, 27 Jun 2020 00:39:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling