Job ID = 8184603 SRX = SRX8047619 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:52:50 prefetch.2.10.7: 1) Downloading 'SRR11471343'... 2020-08-10T04:52:50 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:53:47 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:53:47 prefetch.2.10.7: 1) 'SRR11471343' was downloaded successfully Read 17007226 spots for SRR11471343/SRR11471343.sra Written 17007226 spots for SRR11471343/SRR11471343.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:49 17007226 reads; of these: 17007226 (100.00%) were unpaired; of these: 444755 (2.62%) aligned 0 times 11919324 (70.08%) aligned exactly 1 time 4643147 (27.30%) aligned >1 times 97.38% overall alignment rate Time searching: 00:15:52 Overall time: 00:15:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2374008 / 16562471 = 0.1433 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 @ Mon, 10 Aug 2020 14:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 14:15:18: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:15:18: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:15:24: 1000000 INFO @ Mon, 10 Aug 2020 14:15:30: 2000000 INFO @ Mon, 10 Aug 2020 14:15:35: 3000000 INFO @ Mon, 10 Aug 2020 14:15:41: 4000000 INFO @ Mon, 10 Aug 2020 14:15:47: 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 @ Mon, 10 Aug 2020 14:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 14:15:49: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:15:49: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:15:53: 6000000 INFO @ Mon, 10 Aug 2020 14:15:55: 1000000 INFO @ Mon, 10 Aug 2020 14:15:59: 7000000 INFO @ Mon, 10 Aug 2020 14:16:01: 2000000 INFO @ Mon, 10 Aug 2020 14:16:05: 8000000 INFO @ Mon, 10 Aug 2020 14:16:07: 3000000 INFO @ Mon, 10 Aug 2020 14:16:11: 9000000 INFO @ Mon, 10 Aug 2020 14:16:13: 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 @ Mon, 10 Aug 2020 14:16:17: 10000000 INFO @ Mon, 10 Aug 2020 14:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 14:16:18: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:16:18: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:16:20: 5000000 INFO @ Mon, 10 Aug 2020 14:16:24: 11000000 INFO @ Mon, 10 Aug 2020 14:16:25: 1000000 INFO @ Mon, 10 Aug 2020 14:16:26: 6000000 INFO @ Mon, 10 Aug 2020 14:16:30: 12000000 INFO @ Mon, 10 Aug 2020 14:16:31: 2000000 INFO @ Mon, 10 Aug 2020 14:16:32: 7000000 INFO @ Mon, 10 Aug 2020 14:16:36: 13000000 INFO @ Mon, 10 Aug 2020 14:16:37: 3000000 INFO @ Mon, 10 Aug 2020 14:16:39: 8000000 INFO @ Mon, 10 Aug 2020 14:16:43: 14000000 INFO @ Mon, 10 Aug 2020 14:16:43: 4000000 INFO @ Mon, 10 Aug 2020 14:16:44: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:16:44: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:16:44: #1 total tags in treatment: 14188463 INFO @ Mon, 10 Aug 2020 14:16:44: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:16:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:16:44: #1 tags after filtering in treatment: 14188304 INFO @ Mon, 10 Aug 2020 14:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:16:44: #1 finished! INFO @ Mon, 10 Aug 2020 14:16:44: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:16:45: 9000000 INFO @ Mon, 10 Aug 2020 14:16:46: #2 number of paired peaks: 6407 INFO @ Mon, 10 Aug 2020 14:16:46: start model_add_line... INFO @ Mon, 10 Aug 2020 14:16:46: start X-correlation... INFO @ Mon, 10 Aug 2020 14:16:46: end of X-cor INFO @ Mon, 10 Aug 2020 14:16:46: #2 finished! INFO @ Mon, 10 Aug 2020 14:16:46: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:16:46: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:16:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.05_model.r WARNING @ Mon, 10 Aug 2020 14:16:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:16:46: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:16:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:16:46: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:16:50: 5000000 INFO @ Mon, 10 Aug 2020 14:16:51: 10000000 INFO @ Mon, 10 Aug 2020 14:16:56: 6000000 INFO @ Mon, 10 Aug 2020 14:16:57: 11000000 INFO @ Mon, 10 Aug 2020 14:17:02: 7000000 INFO @ Mon, 10 Aug 2020 14:17:03: 12000000 INFO @ Mon, 10 Aug 2020 14:17:08: 8000000 INFO @ Mon, 10 Aug 2020 14:17:10: 13000000 INFO @ Mon, 10 Aug 2020 14:17:14: 9000000 INFO @ Mon, 10 Aug 2020 14:17:16: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:17:16: 14000000 INFO @ Mon, 10 Aug 2020 14:17:17: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:17:17: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:17:17: #1 total tags in treatment: 14188463 INFO @ Mon, 10 Aug 2020 14:17:17: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:17:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:17:17: #1 tags after filtering in treatment: 14188304 INFO @ Mon, 10 Aug 2020 14:17:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:17:17: #1 finished! INFO @ Mon, 10 Aug 2020 14:17:17: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:17:19: #2 number of paired peaks: 6407 INFO @ Mon, 10 Aug 2020 14:17:19: start model_add_line... INFO @ Mon, 10 Aug 2020 14:17:19: start X-correlation... INFO @ Mon, 10 Aug 2020 14:17:19: end of X-cor INFO @ Mon, 10 Aug 2020 14:17:19: #2 finished! INFO @ Mon, 10 Aug 2020 14:17:19: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:17:19: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:17:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.10_model.r WARNING @ Mon, 10 Aug 2020 14:17:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:17:19: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:17:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:17:19: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:17:20: 10000000 INFO @ Mon, 10 Aug 2020 14:17:26: 11000000 INFO @ Mon, 10 Aug 2020 14:17:31: 12000000 INFO @ Mon, 10 Aug 2020 14:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.05_summits.bed INFO @ Mon, 10 Aug 2020 14:17:32: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1508 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:17:37: 13000000 INFO @ Mon, 10 Aug 2020 14:17:43: 14000000 INFO @ Mon, 10 Aug 2020 14:17:44: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:17:44: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:17:44: #1 total tags in treatment: 14188463 INFO @ Mon, 10 Aug 2020 14:17:44: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:17:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 14:17:44: #1 tags after filtering in treatment: 14188304 INFO @ Mon, 10 Aug 2020 14:17:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:17:44: #1 finished! INFO @ Mon, 10 Aug 2020 14:17:44: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:17:46: #2 number of paired peaks: 6407 INFO @ Mon, 10 Aug 2020 14:17:46: start model_add_line... INFO @ Mon, 10 Aug 2020 14:17:46: start X-correlation... INFO @ Mon, 10 Aug 2020 14:17:46: end of X-cor INFO @ Mon, 10 Aug 2020 14:17:46: #2 finished! INFO @ Mon, 10 Aug 2020 14:17:46: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:17:46: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:17:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.20_model.r WARNING @ Mon, 10 Aug 2020 14:17:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:17:46: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:17:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 14:17:46: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:17:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:17:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:18:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:18:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:18:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.10_summits.bed INFO @ Mon, 10 Aug 2020 14:18:04: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (765 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:18:15: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047619/SRX8047619.20_summits.bed INFO @ Mon, 10 Aug 2020 14:18:31: Done! pass1 - making usageList (26 chroms): 0 millis pass2 - checking and writing primary data (351 records, 4 fields): 2 millis CompletedMACS2peakCalling