Job ID = 6508863 SRX = SRX495236 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:00:14 prefetch.2.10.7: 1) Downloading 'SRR1198741'... 2020-06-26T15:00:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:02:27 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:02:27 prefetch.2.10.7: 1) 'SRR1198741' was downloaded successfully Read 22005854 spots for SRR1198741/SRR1198741.sra Written 22005854 spots for SRR1198741/SRR1198741.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: 00:03:46 22005854 reads; of these: 22005854 (100.00%) were unpaired; of these: 2592713 (11.78%) aligned 0 times 17857324 (81.15%) aligned exactly 1 time 1555817 (7.07%) aligned >1 times 88.22% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 7750526 / 19413141 = 0.3992 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 00:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.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 00:11:14: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:11:14: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:11:20: 1000000 INFO @ Sat, 27 Jun 2020 00:11:26: 2000000 INFO @ Sat, 27 Jun 2020 00:11:31: 3000000 INFO @ Sat, 27 Jun 2020 00:11:37: 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 00:11:42: 5000000 INFO @ Sat, 27 Jun 2020 00:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.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 00:11:44: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:11:44: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:11:49: 6000000 INFO @ Sat, 27 Jun 2020 00:11:52: 1000000 INFO @ Sat, 27 Jun 2020 00:11:55: 7000000 INFO @ Sat, 27 Jun 2020 00:11:59: 2000000 INFO @ Sat, 27 Jun 2020 00:12:02: 8000000 INFO @ Sat, 27 Jun 2020 00:12:05: 3000000 INFO @ Sat, 27 Jun 2020 00:12:09: 9000000 INFO @ Sat, 27 Jun 2020 00:12:12: 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 00:12:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.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 00:12:14: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:12:14: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:12:15: 10000000 INFO @ Sat, 27 Jun 2020 00:12:18: 5000000 INFO @ Sat, 27 Jun 2020 00:12:21: 1000000 INFO @ Sat, 27 Jun 2020 00:12:22: 11000000 INFO @ Sat, 27 Jun 2020 00:12:25: 6000000 INFO @ Sat, 27 Jun 2020 00:12:26: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:12:26: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:12:26: #1 total tags in treatment: 11662615 INFO @ Sat, 27 Jun 2020 00:12:26: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:12:26: #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 00:12:27: #1 tags after filtering in treatment: 11662561 INFO @ Sat, 27 Jun 2020 00:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:12:27: #1 finished! INFO @ Sat, 27 Jun 2020 00:12:27: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:12:27: 2000000 INFO @ Sat, 27 Jun 2020 00:12:28: #2 number of paired peaks: 5641 INFO @ Sat, 27 Jun 2020 00:12:28: start model_add_line... INFO @ Sat, 27 Jun 2020 00:12:28: start X-correlation... INFO @ Sat, 27 Jun 2020 00:12:28: end of X-cor INFO @ Sat, 27 Jun 2020 00:12:28: #2 finished! INFO @ Sat, 27 Jun 2020 00:12:28: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:12:28: #2 alternative fragment length(s) may be 1 bps INFO @ Sat, 27 Jun 2020 00:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.05_model.r WARNING @ Sat, 27 Jun 2020 00:12:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:12:28: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sat, 27 Jun 2020 00:12:28: #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 00:12:28: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:12:31: 7000000 INFO @ Sat, 27 Jun 2020 00:12:34: 3000000 INFO @ Sat, 27 Jun 2020 00:12:38: 8000000 INFO @ Sat, 27 Jun 2020 00:12:40: 4000000 INFO @ Sat, 27 Jun 2020 00:12:44: 9000000 INFO @ Sat, 27 Jun 2020 00:12:47: 5000000 INFO @ Sat, 27 Jun 2020 00:12:50: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:12:51: 10000000 INFO @ Sat, 27 Jun 2020 00:12:53: 6000000 INFO @ Sat, 27 Jun 2020 00:12:57: 11000000 INFO @ Sat, 27 Jun 2020 00:12:59: 7000000 INFO @ Sat, 27 Jun 2020 00:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.05_summits.bed INFO @ Sat, 27 Jun 2020 00:13:00: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:13:02: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:13:02: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:13:02: #1 total tags in treatment: 11662615 INFO @ Sat, 27 Jun 2020 00:13:02: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:13:02: #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 00:13:02: #1 tags after filtering in treatment: 11662561 INFO @ Sat, 27 Jun 2020 00:13:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:13:02: #1 finished! INFO @ Sat, 27 Jun 2020 00:13:02: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:13:02: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:13:04: #2 number of paired peaks: 5641 INFO @ Sat, 27 Jun 2020 00:13:04: start model_add_line... INFO @ Sat, 27 Jun 2020 00:13:04: start X-correlation... INFO @ Sat, 27 Jun 2020 00:13:04: end of X-cor INFO @ Sat, 27 Jun 2020 00:13:04: #2 finished! INFO @ Sat, 27 Jun 2020 00:13:04: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:13:04: #2 alternative fragment length(s) may be 1 bps INFO @ Sat, 27 Jun 2020 00:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.10_model.r WARNING @ Sat, 27 Jun 2020 00:13:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:13:04: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sat, 27 Jun 2020 00:13:04: #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 00:13:04: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:13:05: 8000000 INFO @ Sat, 27 Jun 2020 00:13:11: 9000000 INFO @ Sat, 27 Jun 2020 00:13:17: 10000000 INFO @ Sat, 27 Jun 2020 00:13:23: 11000000 INFO @ Sat, 27 Jun 2020 00:13:25: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:13:27: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:13:27: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:13:27: #1 total tags in treatment: 11662615 INFO @ Sat, 27 Jun 2020 00:13:27: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:13:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:13:27: #1 tags after filtering in treatment: 11662561 INFO @ Sat, 27 Jun 2020 00:13:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:13:27: #1 finished! INFO @ Sat, 27 Jun 2020 00:13:27: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:13:29: #2 number of paired peaks: 5641 INFO @ Sat, 27 Jun 2020 00:13:29: start model_add_line... INFO @ Sat, 27 Jun 2020 00:13:29: start X-correlation... INFO @ Sat, 27 Jun 2020 00:13:29: end of X-cor INFO @ Sat, 27 Jun 2020 00:13:29: #2 finished! INFO @ Sat, 27 Jun 2020 00:13:29: #2 predicted fragment length is 1 bps INFO @ Sat, 27 Jun 2020 00:13:29: #2 alternative fragment length(s) may be 1 bps INFO @ Sat, 27 Jun 2020 00:13:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.20_model.r WARNING @ Sat, 27 Jun 2020 00:13:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:13:29: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sat, 27 Jun 2020 00:13:29: #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 00:13:29: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:13:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.10_summits.bed INFO @ Sat, 27 Jun 2020 00:13:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:13:50: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495236/SRX495236.20_summits.bed INFO @ Sat, 27 Jun 2020 00:14:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling