Job ID = 8184618 SRX = SRX8047628 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:59:49 prefetch.2.10.7: 1) Downloading 'SRR11471352'... 2020-08-10T04:59:49 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T05:00:54 prefetch.2.10.7: HTTPS download succeed 2020-08-10T05:00:54 prefetch.2.10.7: 1) 'SRR11471352' was downloaded successfully Read 21052691 spots for SRR11471352/SRR11471352.sra Written 21052691 spots for SRR11471352/SRR11471352.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: 00:00:01 Multiseed full-index search: 00:18:46 21052691 reads; of these: 21052691 (100.00%) were unpaired; of these: 569762 (2.71%) aligned 0 times 14630944 (69.50%) aligned exactly 1 time 5851985 (27.80%) aligned >1 times 97.29% overall alignment rate Time searching: 00:18:48 Overall time: 00:18:48 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 12 files... [bam_rmdupse_core] 632797 / 20482929 = 0.0309 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 14:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.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 14:26:39: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:26:39: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:26:44: 1000000 INFO @ Mon, 10 Aug 2020 14:26:49: 2000000 INFO @ Mon, 10 Aug 2020 14:26:54: 3000000 INFO @ Mon, 10 Aug 2020 14:26:58: 4000000 INFO @ Mon, 10 Aug 2020 14:27:03: 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 14:27:08: 6000000 INFO @ Mon, 10 Aug 2020 14:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.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 14:27:09: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:27:09: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:27:13: 7000000 INFO @ Mon, 10 Aug 2020 14:27:14: 1000000 INFO @ Mon, 10 Aug 2020 14:27:18: 8000000 INFO @ Mon, 10 Aug 2020 14:27:19: 2000000 INFO @ Mon, 10 Aug 2020 14:27:24: 9000000 INFO @ Mon, 10 Aug 2020 14:27:24: 3000000 INFO @ Mon, 10 Aug 2020 14:27:29: 10000000 INFO @ Mon, 10 Aug 2020 14:27:29: 4000000 INFO @ Mon, 10 Aug 2020 14:27:34: 11000000 INFO @ Mon, 10 Aug 2020 14:27:34: 5000000 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 14:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.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 14:27:39: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:27:39: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:27:39: 12000000 INFO @ Mon, 10 Aug 2020 14:27:39: 6000000 INFO @ Mon, 10 Aug 2020 14:27:44: 1000000 INFO @ Mon, 10 Aug 2020 14:27:44: 13000000 INFO @ Mon, 10 Aug 2020 14:27:44: 7000000 INFO @ Mon, 10 Aug 2020 14:27:49: 2000000 INFO @ Mon, 10 Aug 2020 14:27:49: 14000000 INFO @ Mon, 10 Aug 2020 14:27:49: 8000000 INFO @ Mon, 10 Aug 2020 14:27:54: 3000000 INFO @ Mon, 10 Aug 2020 14:27:54: 15000000 INFO @ Mon, 10 Aug 2020 14:27:54: 9000000 INFO @ Mon, 10 Aug 2020 14:27:59: 4000000 INFO @ Mon, 10 Aug 2020 14:27:59: 16000000 INFO @ Mon, 10 Aug 2020 14:28:00: 10000000 INFO @ Mon, 10 Aug 2020 14:28:04: 5000000 INFO @ Mon, 10 Aug 2020 14:28:04: 17000000 INFO @ Mon, 10 Aug 2020 14:28:05: 11000000 INFO @ Mon, 10 Aug 2020 14:28:09: 6000000 INFO @ Mon, 10 Aug 2020 14:28:09: 18000000 INFO @ Mon, 10 Aug 2020 14:28:10: 12000000 INFO @ Mon, 10 Aug 2020 14:28:14: 7000000 INFO @ Mon, 10 Aug 2020 14:28:15: 19000000 INFO @ Mon, 10 Aug 2020 14:28:15: 13000000 INFO @ Mon, 10 Aug 2020 14:28:19: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:28:19: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:28:19: #1 total tags in treatment: 19850132 INFO @ Mon, 10 Aug 2020 14:28:19: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:28:19: #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 14:28:20: 8000000 INFO @ Mon, 10 Aug 2020 14:28:20: #1 tags after filtering in treatment: 19849997 INFO @ Mon, 10 Aug 2020 14:28:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:28:20: #1 finished! INFO @ Mon, 10 Aug 2020 14:28:20: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:28:20: 14000000 INFO @ Mon, 10 Aug 2020 14:28:22: #2 number of paired peaks: 6393 INFO @ Mon, 10 Aug 2020 14:28:22: start model_add_line... INFO @ Mon, 10 Aug 2020 14:28:22: start X-correlation... INFO @ Mon, 10 Aug 2020 14:28:22: end of X-cor INFO @ Mon, 10 Aug 2020 14:28:22: #2 finished! INFO @ Mon, 10 Aug 2020 14:28:22: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:28:22: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.05_model.r WARNING @ Mon, 10 Aug 2020 14:28:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:28:22: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:28:22: #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 14:28:22: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:28:25: 9000000 INFO @ Mon, 10 Aug 2020 14:28:25: 15000000 INFO @ Mon, 10 Aug 2020 14:28:30: 10000000 INFO @ Mon, 10 Aug 2020 14:28:30: 16000000 INFO @ Mon, 10 Aug 2020 14:28:35: 11000000 INFO @ Mon, 10 Aug 2020 14:28:35: 17000000 INFO @ Mon, 10 Aug 2020 14:28:40: 12000000 INFO @ Mon, 10 Aug 2020 14:28:40: 18000000 INFO @ Mon, 10 Aug 2020 14:28:45: 13000000 INFO @ Mon, 10 Aug 2020 14:28:45: 19000000 INFO @ Mon, 10 Aug 2020 14:28:50: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:28:50: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:28:50: #1 total tags in treatment: 19850132 INFO @ Mon, 10 Aug 2020 14:28:50: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:28:50: #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 14:28:50: 14000000 INFO @ Mon, 10 Aug 2020 14:28:50: #1 tags after filtering in treatment: 19849997 INFO @ Mon, 10 Aug 2020 14:28:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:28:50: #1 finished! INFO @ Mon, 10 Aug 2020 14:28:50: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:28:52: #2 number of paired peaks: 6393 INFO @ Mon, 10 Aug 2020 14:28:52: start model_add_line... INFO @ Mon, 10 Aug 2020 14:28:52: start X-correlation... INFO @ Mon, 10 Aug 2020 14:28:52: end of X-cor INFO @ Mon, 10 Aug 2020 14:28:52: #2 finished! INFO @ Mon, 10 Aug 2020 14:28:52: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:28:52: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:28:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.10_model.r WARNING @ Mon, 10 Aug 2020 14:28:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:28:52: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:28:52: #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 14:28:52: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:28:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:28:55: 15000000 INFO @ Mon, 10 Aug 2020 14:29:00: 16000000 INFO @ Mon, 10 Aug 2020 14:29:03: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:29:05: 17000000 INFO @ Mon, 10 Aug 2020 14:29:10: 18000000 INFO @ Mon, 10 Aug 2020 14:29:15: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:29:19: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:29:19: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:29:19: #1 total tags in treatment: 19850132 INFO @ Mon, 10 Aug 2020 14:29:19: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:29:19: #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 14:29:20: #1 tags after filtering in treatment: 19849997 INFO @ Mon, 10 Aug 2020 14:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:29:20: #1 finished! INFO @ Mon, 10 Aug 2020 14:29:20: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:29:22: #2 number of paired peaks: 6393 INFO @ Mon, 10 Aug 2020 14:29:22: start model_add_line... INFO @ Mon, 10 Aug 2020 14:29:22: start X-correlation... INFO @ Mon, 10 Aug 2020 14:29:22: end of X-cor INFO @ Mon, 10 Aug 2020 14:29:22: #2 finished! INFO @ Mon, 10 Aug 2020 14:29:22: #2 predicted fragment length is 51 bps INFO @ Mon, 10 Aug 2020 14:29:22: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 10 Aug 2020 14:29:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.20_model.r WARNING @ Mon, 10 Aug 2020 14:29:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:29:22: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 10 Aug 2020 14:29:22: #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 14:29:22: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:29:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:29:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:29:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.05_summits.bed INFO @ Mon, 10 Aug 2020 14:29:24: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (2260 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:29:33: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.10_summits.bed INFO @ Mon, 10 Aug 2020 14:29:54: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (1049 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:30:02: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:30:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:30:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:30:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047628/SRX8047628.20_summits.bed INFO @ Mon, 10 Aug 2020 14:30:23: Done! pass1 - making usageList (32 chroms): 0 millis pass2 - checking and writing primary data (480 records, 4 fields): 3 millis CompletedMACS2peakCalling