Job ID = 6508887 SRX = SRX495282 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:57:29 prefetch.2.10.7: 1) Downloading 'SRR1198787'... 2020-06-26T14:57:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:58:33 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:58:34 prefetch.2.10.7: 'SRR1198787' is valid 2020-06-26T14:58:34 prefetch.2.10.7: 1) 'SRR1198787' was downloaded successfully Read 12316588 spots for SRR1198787/SRR1198787.sra Written 12316588 spots for SRR1198787/SRR1198787.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: 00:03:08 12316588 reads; of these: 12316588 (100.00%) were unpaired; of these: 806172 (6.55%) aligned 0 times 10656857 (86.52%) aligned exactly 1 time 853559 (6.93%) aligned >1 times 93.45% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 2961900 / 11510416 = 0.2573 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 00:05:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.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 00:05:10: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:05:10: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:05:16: 1000000 INFO @ Sat, 27 Jun 2020 00:05:21: 2000000 INFO @ Sat, 27 Jun 2020 00:05:27: 3000000 INFO @ Sat, 27 Jun 2020 00:05:32: 4000000 INFO @ Sat, 27 Jun 2020 00:05:38: 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 @ Sat, 27 Jun 2020 00:05:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.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 00:05:40: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:05:40: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:05:44: 6000000 INFO @ Sat, 27 Jun 2020 00:05:46: 1000000 INFO @ Sat, 27 Jun 2020 00:05:50: 7000000 INFO @ Sat, 27 Jun 2020 00:05:52: 2000000 INFO @ Sat, 27 Jun 2020 00:05:56: 8000000 INFO @ Sat, 27 Jun 2020 00:05:58: 3000000 INFO @ Sat, 27 Jun 2020 00:06:00: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:06:00: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:06:00: #1 total tags in treatment: 8548516 INFO @ Sat, 27 Jun 2020 00:06:00: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:06:00: #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 00:06:00: #1 tags after filtering in treatment: 8548124 INFO @ Sat, 27 Jun 2020 00:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:06:00: #1 finished! INFO @ Sat, 27 Jun 2020 00:06:00: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:06:01: #2 number of paired peaks: 2521 INFO @ Sat, 27 Jun 2020 00:06:01: start model_add_line... INFO @ Sat, 27 Jun 2020 00:06:01: start X-correlation... INFO @ Sat, 27 Jun 2020 00:06:01: end of X-cor INFO @ Sat, 27 Jun 2020 00:06:01: #2 finished! INFO @ Sat, 27 Jun 2020 00:06:01: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:06:01: #2 alternative fragment length(s) may be 2 bps INFO @ Sat, 27 Jun 2020 00:06:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.05_model.r WARNING @ Sat, 27 Jun 2020 00:06:01: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:06:01: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sat, 27 Jun 2020 00:06:01: #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 00:06:01: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:06:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:06:04: 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 00:06:10: 5000000 INFO @ Sat, 27 Jun 2020 00:06:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.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 00:06:10: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:06:10: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:06:16: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:06:17: 6000000 INFO @ Sat, 27 Jun 2020 00:06:18: 1000000 INFO @ Sat, 27 Jun 2020 00:06:23: 7000000 INFO @ Sat, 27 Jun 2020 00:06:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:06:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:06:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.05_summits.bed INFO @ Sat, 27 Jun 2020 00:06:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:06:25: 2000000 INFO @ Sat, 27 Jun 2020 00:06:30: 8000000 INFO @ Sat, 27 Jun 2020 00:06:32: 3000000 INFO @ Sat, 27 Jun 2020 00:06:34: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:06:34: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:06:34: #1 total tags in treatment: 8548516 INFO @ Sat, 27 Jun 2020 00:06:34: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:06:34: #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 00:06:34: #1 tags after filtering in treatment: 8548124 INFO @ Sat, 27 Jun 2020 00:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:06:34: #1 finished! INFO @ Sat, 27 Jun 2020 00:06:34: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:06:35: #2 number of paired peaks: 2521 INFO @ Sat, 27 Jun 2020 00:06:35: start model_add_line... INFO @ Sat, 27 Jun 2020 00:06:35: start X-correlation... INFO @ Sat, 27 Jun 2020 00:06:35: end of X-cor INFO @ Sat, 27 Jun 2020 00:06:35: #2 finished! INFO @ Sat, 27 Jun 2020 00:06:35: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:06:35: #2 alternative fragment length(s) may be 2 bps INFO @ Sat, 27 Jun 2020 00:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.10_model.r WARNING @ Sat, 27 Jun 2020 00:06:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:06:35: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sat, 27 Jun 2020 00:06:35: #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 00:06:35: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:06:39: 4000000 INFO @ Sat, 27 Jun 2020 00:06:46: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:06:50: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:06:53: 6000000 INFO @ Sat, 27 Jun 2020 00:06:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:06:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:06:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.10_summits.bed INFO @ Sat, 27 Jun 2020 00:06:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:07:00: 7000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:07:06: 8000000 INFO @ Sat, 27 Jun 2020 00:07:10: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:07:10: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:07:10: #1 total tags in treatment: 8548516 INFO @ Sat, 27 Jun 2020 00:07:10: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:07:10: #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 00:07:10: #1 tags after filtering in treatment: 8548124 INFO @ Sat, 27 Jun 2020 00:07:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:07:10: #1 finished! INFO @ Sat, 27 Jun 2020 00:07:10: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:07:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:07:11: #2 number of paired peaks: 2521 INFO @ Sat, 27 Jun 2020 00:07:11: start model_add_line... INFO @ Sat, 27 Jun 2020 00:07:11: start X-correlation... INFO @ Sat, 27 Jun 2020 00:07:11: end of X-cor INFO @ Sat, 27 Jun 2020 00:07:11: #2 finished! INFO @ Sat, 27 Jun 2020 00:07:11: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:07:11: #2 alternative fragment length(s) may be 2 bps INFO @ Sat, 27 Jun 2020 00:07:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.20_model.r WARNING @ Sat, 27 Jun 2020 00:07:11: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:07:11: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sat, 27 Jun 2020 00:07:11: #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 00:07:11: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:07:27: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495282/SRX495282.20_summits.bed INFO @ Sat, 27 Jun 2020 00:07:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling