Job ID = 6498400 SRX = SRX495235 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:04:55 prefetch.2.10.7: 1) Downloading 'SRR1198740'... 2020-06-26T00:04:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:07:10 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:07:10 prefetch.2.10.7: 1) 'SRR1198740' was downloaded successfully Read 22984833 spots for SRR1198740/SRR1198740.sra Written 22984833 spots for SRR1198740/SRR1198740.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: 00:04:14 22984833 reads; of these: 22984833 (100.00%) were unpaired; of these: 1369171 (5.96%) aligned 0 times 20057705 (87.26%) aligned exactly 1 time 1557957 (6.78%) aligned >1 times 94.04% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 9025532 / 21615662 = 0.4175 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 09:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.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 09:18:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:16: 1000000 INFO @ Fri, 26 Jun 2020 09:18:22: 2000000 INFO @ Fri, 26 Jun 2020 09:18:29: 3000000 INFO @ Fri, 26 Jun 2020 09:18:36: 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 09:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.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 09:18:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:43: 5000000 INFO @ Fri, 26 Jun 2020 09:18:47: 1000000 INFO @ Fri, 26 Jun 2020 09:18:50: 6000000 INFO @ Fri, 26 Jun 2020 09:18:55: 2000000 INFO @ Fri, 26 Jun 2020 09:18:57: 7000000 INFO @ Fri, 26 Jun 2020 09:19:02: 3000000 INFO @ Fri, 26 Jun 2020 09:19:05: 8000000 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 09:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.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 09:19:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:19:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:19:10: 4000000 INFO @ Fri, 26 Jun 2020 09:19:12: 9000000 INFO @ Fri, 26 Jun 2020 09:19:16: 1000000 INFO @ Fri, 26 Jun 2020 09:19:17: 5000000 INFO @ Fri, 26 Jun 2020 09:19:20: 10000000 INFO @ Fri, 26 Jun 2020 09:19:23: 2000000 INFO @ Fri, 26 Jun 2020 09:19:25: 6000000 INFO @ Fri, 26 Jun 2020 09:19:28: 11000000 INFO @ Fri, 26 Jun 2020 09:19:30: 3000000 INFO @ Fri, 26 Jun 2020 09:19:33: 7000000 INFO @ Fri, 26 Jun 2020 09:19:36: 12000000 INFO @ Fri, 26 Jun 2020 09:19:37: 4000000 INFO @ Fri, 26 Jun 2020 09:19:40: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:19:40: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:19:40: #1 total tags in treatment: 12590130 INFO @ Fri, 26 Jun 2020 09:19:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:40: #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 09:19:40: #1 tags after filtering in treatment: 12590130 INFO @ Fri, 26 Jun 2020 09:19:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:19:40: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:41: 8000000 INFO @ Fri, 26 Jun 2020 09:19:42: #2 number of paired peaks: 4139 INFO @ Fri, 26 Jun 2020 09:19:42: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:42: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:42: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:42: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:42: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:19:42: #2 alternative fragment length(s) may be 2,577,594,597 bps INFO @ Fri, 26 Jun 2020 09:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.05_model.r WARNING @ Fri, 26 Jun 2020 09:19:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:19:42: #2 You may need to consider one of the other alternative d(s): 2,577,594,597 WARNING @ Fri, 26 Jun 2020 09:19:42: #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 09:19:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:19:44: 5000000 INFO @ Fri, 26 Jun 2020 09:19:48: 9000000 INFO @ Fri, 26 Jun 2020 09:19:51: 6000000 INFO @ Fri, 26 Jun 2020 09:19:55: 10000000 INFO @ Fri, 26 Jun 2020 09:19:58: 7000000 INFO @ Fri, 26 Jun 2020 09:20:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:20:02: 11000000 INFO @ Fri, 26 Jun 2020 09:20:05: 8000000 INFO @ Fri, 26 Jun 2020 09:20:10: 12000000 INFO @ Fri, 26 Jun 2020 09:20:12: 9000000 INFO @ Fri, 26 Jun 2020 09:20:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:20:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:20:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.05_summits.bed INFO @ Fri, 26 Jun 2020 09:20:13: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:20:14: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:20:14: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:20:14: #1 total tags in treatment: 12590130 INFO @ Fri, 26 Jun 2020 09:20:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:20:14: #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 09:20:14: #1 tags after filtering in treatment: 12590130 INFO @ Fri, 26 Jun 2020 09:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:20:14: #1 finished! INFO @ Fri, 26 Jun 2020 09:20:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:20:14: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:20:15: #2 number of paired peaks: 4139 INFO @ Fri, 26 Jun 2020 09:20:15: start model_add_line... INFO @ Fri, 26 Jun 2020 09:20:15: start X-correlation... INFO @ Fri, 26 Jun 2020 09:20:15: end of X-cor INFO @ Fri, 26 Jun 2020 09:20:15: #2 finished! INFO @ Fri, 26 Jun 2020 09:20:15: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:20:15: #2 alternative fragment length(s) may be 2,577,594,597 bps INFO @ Fri, 26 Jun 2020 09:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.10_model.r WARNING @ Fri, 26 Jun 2020 09:20:15: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:20:15: #2 You may need to consider one of the other alternative d(s): 2,577,594,597 WARNING @ Fri, 26 Jun 2020 09:20:15: #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 09:20:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:20:19: 10000000 INFO @ Fri, 26 Jun 2020 09:20:26: 11000000 INFO @ Fri, 26 Jun 2020 09:20:33: 12000000 INFO @ Fri, 26 Jun 2020 09:20:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:20:37: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:20:37: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:20:37: #1 total tags in treatment: 12590130 INFO @ Fri, 26 Jun 2020 09:20:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:20:37: #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 09:20:37: #1 tags after filtering in treatment: 12590130 INFO @ Fri, 26 Jun 2020 09:20:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:20:37: #1 finished! INFO @ Fri, 26 Jun 2020 09:20:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:20:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:20:38: #2 number of paired peaks: 4139 INFO @ Fri, 26 Jun 2020 09:20:38: start model_add_line... INFO @ Fri, 26 Jun 2020 09:20:38: start X-correlation... INFO @ Fri, 26 Jun 2020 09:20:38: end of X-cor INFO @ Fri, 26 Jun 2020 09:20:38: #2 finished! INFO @ Fri, 26 Jun 2020 09:20:38: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:20:38: #2 alternative fragment length(s) may be 2,577,594,597 bps INFO @ Fri, 26 Jun 2020 09:20:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.20_model.r WARNING @ Fri, 26 Jun 2020 09:20:38: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:20:38: #2 You may need to consider one of the other alternative d(s): 2,577,594,597 WARNING @ Fri, 26 Jun 2020 09:20:38: #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 09:20:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:20:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:20:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:20:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:20:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.10_summits.bed INFO @ Fri, 26 Jun 2020 09:20:46: 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 09:20:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:21:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:21:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:21:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495235/SRX495235.20_summits.bed INFO @ Fri, 26 Jun 2020 09:21:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling