Job ID = 6498420 SRX = SRX495277 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:51:36 prefetch.2.10.7: 1) Downloading 'SRR1198782'... 2020-06-25T23:51:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:26 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:26 prefetch.2.10.7: 1) 'SRR1198782' was downloaded successfully Read 26442280 spots for SRR1198782/SRR1198782.sra Written 26442280 spots for SRR1198782/SRR1198782.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: 00:10:56 26442280 reads; of these: 26442280 (100.00%) were unpaired; of these: 1370123 (5.18%) aligned 0 times 10227747 (38.68%) aligned exactly 1 time 14844410 (56.14%) aligned >1 times 94.82% overall alignment rate Time searching: 00:10:57 Overall time: 00:10:57 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 12 files... [bam_rmdupse_core] 12445505 / 25072157 = 0.4964 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 09:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.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 09:13:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:13:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:13:12: 1000000 INFO @ Fri, 26 Jun 2020 09:13:19: 2000000 INFO @ Fri, 26 Jun 2020 09:13:25: 3000000 INFO @ Fri, 26 Jun 2020 09:13:31: 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 09:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.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 09:13:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:13:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:13:37: 5000000 INFO @ Fri, 26 Jun 2020 09:13:42: 1000000 INFO @ Fri, 26 Jun 2020 09:13:43: 6000000 INFO @ Fri, 26 Jun 2020 09:13:49: 2000000 INFO @ Fri, 26 Jun 2020 09:13:49: 7000000 INFO @ Fri, 26 Jun 2020 09:13:55: 3000000 INFO @ Fri, 26 Jun 2020 09:13:56: 8000000 INFO @ Fri, 26 Jun 2020 09:14:02: 4000000 INFO @ Fri, 26 Jun 2020 09:14:02: 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 09:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.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 09:14:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:14:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:14:08: 5000000 INFO @ Fri, 26 Jun 2020 09:14:09: 10000000 INFO @ Fri, 26 Jun 2020 09:14:12: 1000000 INFO @ Fri, 26 Jun 2020 09:14:15: 6000000 INFO @ Fri, 26 Jun 2020 09:14:15: 11000000 INFO @ Fri, 26 Jun 2020 09:14:19: 2000000 INFO @ Fri, 26 Jun 2020 09:14:21: 7000000 INFO @ Fri, 26 Jun 2020 09:14:22: 12000000 INFO @ Fri, 26 Jun 2020 09:14:26: 3000000 INFO @ Fri, 26 Jun 2020 09:14:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:14:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:14:26: #1 total tags in treatment: 12626652 INFO @ Fri, 26 Jun 2020 09:14:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:14:26: #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 09:14:26: #1 tags after filtering in treatment: 12626652 INFO @ Fri, 26 Jun 2020 09:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:14:26: #1 finished! INFO @ Fri, 26 Jun 2020 09:14:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:14:28: 8000000 INFO @ Fri, 26 Jun 2020 09:14:28: #2 number of paired peaks: 3222 INFO @ Fri, 26 Jun 2020 09:14:28: start model_add_line... INFO @ Fri, 26 Jun 2020 09:14:28: start X-correlation... INFO @ Fri, 26 Jun 2020 09:14:28: end of X-cor INFO @ Fri, 26 Jun 2020 09:14:28: #2 finished! INFO @ Fri, 26 Jun 2020 09:14:28: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:14:28: #2 alternative fragment length(s) may be 2,13 bps INFO @ Fri, 26 Jun 2020 09:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.05_model.r WARNING @ Fri, 26 Jun 2020 09:14:28: #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 09:14:28: #2 You may need to consider one of the other alternative d(s): 2,13 WARNING @ Fri, 26 Jun 2020 09:14:28: #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 09:14:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:14:32: 4000000 INFO @ Fri, 26 Jun 2020 09:14:34: 9000000 INFO @ Fri, 26 Jun 2020 09:14:39: 5000000 INFO @ Fri, 26 Jun 2020 09:14:41: 10000000 INFO @ Fri, 26 Jun 2020 09:14:45: 6000000 INFO @ Fri, 26 Jun 2020 09:14:47: 11000000 INFO @ Fri, 26 Jun 2020 09:14:52: 7000000 INFO @ Fri, 26 Jun 2020 09:14:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:14:54: 12000000 INFO @ Fri, 26 Jun 2020 09:14:58: 8000000 INFO @ Fri, 26 Jun 2020 09:14:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:14:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:14:58: #1 total tags in treatment: 12626652 INFO @ Fri, 26 Jun 2020 09:14:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:14:58: #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 09:14:58: #1 tags after filtering in treatment: 12626652 INFO @ Fri, 26 Jun 2020 09:14:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:14:58: #1 finished! INFO @ Fri, 26 Jun 2020 09:14:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:14:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:15:00: #2 number of paired peaks: 3222 INFO @ Fri, 26 Jun 2020 09:15:00: start model_add_line... INFO @ Fri, 26 Jun 2020 09:15:00: start X-correlation... INFO @ Fri, 26 Jun 2020 09:15:00: end of X-cor INFO @ Fri, 26 Jun 2020 09:15:00: #2 finished! INFO @ Fri, 26 Jun 2020 09:15:00: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:15:00: #2 alternative fragment length(s) may be 2,13 bps INFO @ Fri, 26 Jun 2020 09:15:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.10_model.r WARNING @ Fri, 26 Jun 2020 09:15:00: #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 09:15:00: #2 You may need to consider one of the other alternative d(s): 2,13 WARNING @ Fri, 26 Jun 2020 09:15:00: #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 09:15:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:15:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:15:04: 9000000 INFO @ Fri, 26 Jun 2020 09:15:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:15:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:15:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.05_summits.bed INFO @ Fri, 26 Jun 2020 09:15:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:15:11: 10000000 INFO @ Fri, 26 Jun 2020 09:15:17: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:15:23: 12000000 INFO @ Fri, 26 Jun 2020 09:15:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:15:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:15:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:15:27: #1 total tags in treatment: 12626652 INFO @ Fri, 26 Jun 2020 09:15:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:15:27: #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 09:15:28: #1 tags after filtering in treatment: 12626652 INFO @ Fri, 26 Jun 2020 09:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:15:28: #1 finished! INFO @ Fri, 26 Jun 2020 09:15:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:15:29: #2 number of paired peaks: 3222 INFO @ Fri, 26 Jun 2020 09:15:29: start model_add_line... INFO @ Fri, 26 Jun 2020 09:15:29: start X-correlation... INFO @ Fri, 26 Jun 2020 09:15:29: end of X-cor INFO @ Fri, 26 Jun 2020 09:15:29: #2 finished! INFO @ Fri, 26 Jun 2020 09:15:29: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:15:29: #2 alternative fragment length(s) may be 2,13 bps INFO @ Fri, 26 Jun 2020 09:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.20_model.r WARNING @ Fri, 26 Jun 2020 09:15:29: #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 09:15:29: #2 You may need to consider one of the other alternative d(s): 2,13 WARNING @ Fri, 26 Jun 2020 09:15:29: #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 09:15:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.10_summits.bed INFO @ Fri, 26 Jun 2020 09:15:39: 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 09:15:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495277/SRX495277.20_summits.bed INFO @ Fri, 26 Jun 2020 09:16:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling