Job ID = 8184608 SRX = SRX8047621 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:53:19 prefetch.2.10.7: 1) Downloading 'SRR11471345'... 2020-08-10T04:53:19 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:54:16 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:54:16 prefetch.2.10.7: 1) 'SRR11471345' was downloaded successfully Read 18431278 spots for SRR11471345/SRR11471345.sra Written 18431278 spots for SRR11471345/SRR11471345.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:16:05 18431278 reads; of these: 18431278 (100.00%) were unpaired; of these: 527277 (2.86%) aligned 0 times 12838838 (69.66%) aligned exactly 1 time 5065163 (27.48%) aligned >1 times 97.14% overall alignment rate Time searching: 00:16:07 Overall time: 00:16:07 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] 3010509 / 17904001 = 0.1681 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 14:16:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.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 14:16:31: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:16:31: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:16:37: 1000000 INFO @ Mon, 10 Aug 2020 14:16:42: 2000000 INFO @ Mon, 10 Aug 2020 14:16:47: 3000000 INFO @ Mon, 10 Aug 2020 14:16:52: 4000000 INFO @ Mon, 10 Aug 2020 14:16:58: 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 14:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.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 14:17:01: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:17:01: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:17:03: 6000000 INFO @ Mon, 10 Aug 2020 14:17:08: 1000000 INFO @ Mon, 10 Aug 2020 14:17:09: 7000000 INFO @ Mon, 10 Aug 2020 14:17:14: 8000000 INFO @ Mon, 10 Aug 2020 14:17:14: 2000000 INFO @ Mon, 10 Aug 2020 14:17:20: 9000000 INFO @ Mon, 10 Aug 2020 14:17:21: 3000000 INFO @ Mon, 10 Aug 2020 14:17:25: 10000000 INFO @ Mon, 10 Aug 2020 14:17:27: 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 14:17:31: 11000000 INFO @ Mon, 10 Aug 2020 14:17:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.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 14:17:31: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:17:31: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:17:34: 5000000 INFO @ Mon, 10 Aug 2020 14:17:37: 12000000 INFO @ Mon, 10 Aug 2020 14:17:37: 1000000 INFO @ Mon, 10 Aug 2020 14:17:41: 6000000 INFO @ Mon, 10 Aug 2020 14:17:43: 13000000 INFO @ Mon, 10 Aug 2020 14:17:43: 2000000 INFO @ Mon, 10 Aug 2020 14:17:47: 7000000 INFO @ Mon, 10 Aug 2020 14:17:49: 14000000 INFO @ Mon, 10 Aug 2020 14:17:49: 3000000 INFO @ Mon, 10 Aug 2020 14:17:54: 8000000 INFO @ Mon, 10 Aug 2020 14:17:54: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:17:54: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:17:54: #1 total tags in treatment: 14893492 INFO @ Mon, 10 Aug 2020 14:17:54: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:17:54: #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 14:17:54: #1 tags after filtering in treatment: 14893338 INFO @ Mon, 10 Aug 2020 14:17:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:17:54: #1 finished! INFO @ Mon, 10 Aug 2020 14:17:54: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:17:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:17:55: 4000000 INFO @ Mon, 10 Aug 2020 14:17:56: #2 number of paired peaks: 6374 INFO @ Mon, 10 Aug 2020 14:17:56: start model_add_line... INFO @ Mon, 10 Aug 2020 14:17:56: start X-correlation... INFO @ Mon, 10 Aug 2020 14:17:56: end of X-cor INFO @ Mon, 10 Aug 2020 14:17:56: #2 finished! INFO @ Mon, 10 Aug 2020 14:17:56: #2 predicted fragment length is 50 bps INFO @ Mon, 10 Aug 2020 14:17:56: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 10 Aug 2020 14:17:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.05_model.r WARNING @ Mon, 10 Aug 2020 14:17:56: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:17:56: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 10 Aug 2020 14:17:56: #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 14:17:56: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:17:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:18:00: 9000000 INFO @ Mon, 10 Aug 2020 14:18:01: 5000000 INFO @ Mon, 10 Aug 2020 14:18:07: 10000000 INFO @ Mon, 10 Aug 2020 14:18:07: 6000000 INFO @ Mon, 10 Aug 2020 14:18:13: 7000000 INFO @ Mon, 10 Aug 2020 14:18:13: 11000000 INFO @ Mon, 10 Aug 2020 14:18:20: 8000000 INFO @ Mon, 10 Aug 2020 14:18:20: 12000000 INFO @ Mon, 10 Aug 2020 14:18:26: 9000000 INFO @ Mon, 10 Aug 2020 14:18:27: 13000000 INFO @ Mon, 10 Aug 2020 14:18:32: 10000000 INFO @ Mon, 10 Aug 2020 14:18:33: 14000000 INFO @ Mon, 10 Aug 2020 14:18:34: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:18:39: 11000000 INFO @ Mon, 10 Aug 2020 14:18:39: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:18:39: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:18:39: #1 total tags in treatment: 14893492 INFO @ Mon, 10 Aug 2020 14:18:39: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:18:39: #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 14:18:40: #1 tags after filtering in treatment: 14893338 INFO @ Mon, 10 Aug 2020 14:18:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:18:40: #1 finished! INFO @ Mon, 10 Aug 2020 14:18:40: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:18:42: #2 number of paired peaks: 6374 INFO @ Mon, 10 Aug 2020 14:18:42: start model_add_line... INFO @ Mon, 10 Aug 2020 14:18:42: start X-correlation... INFO @ Mon, 10 Aug 2020 14:18:42: end of X-cor INFO @ Mon, 10 Aug 2020 14:18:42: #2 finished! INFO @ Mon, 10 Aug 2020 14:18:42: #2 predicted fragment length is 50 bps INFO @ Mon, 10 Aug 2020 14:18:42: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 10 Aug 2020 14:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.10_model.r WARNING @ Mon, 10 Aug 2020 14:18:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:18:42: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 10 Aug 2020 14:18:42: #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 14:18:42: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:18:44: 12000000 INFO @ Mon, 10 Aug 2020 14:18:49: 13000000 INFO @ Mon, 10 Aug 2020 14:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.05_summits.bed INFO @ Mon, 10 Aug 2020 14:18:52: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1473 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:18:55: 14000000 INFO @ Mon, 10 Aug 2020 14:19:00: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:19:00: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:19:00: #1 total tags in treatment: 14893492 INFO @ Mon, 10 Aug 2020 14:19:00: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:19:00: #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 14:19:00: #1 tags after filtering in treatment: 14893338 INFO @ Mon, 10 Aug 2020 14:19:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:19:00: #1 finished! INFO @ Mon, 10 Aug 2020 14:19:00: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:19:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:19:02: #2 number of paired peaks: 6374 INFO @ Mon, 10 Aug 2020 14:19:02: start model_add_line... INFO @ Mon, 10 Aug 2020 14:19:02: start X-correlation... INFO @ Mon, 10 Aug 2020 14:19:02: end of X-cor INFO @ Mon, 10 Aug 2020 14:19:02: #2 finished! INFO @ Mon, 10 Aug 2020 14:19:02: #2 predicted fragment length is 50 bps INFO @ Mon, 10 Aug 2020 14:19:02: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 10 Aug 2020 14:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.20_model.r WARNING @ Mon, 10 Aug 2020 14:19:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:19:02: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 10 Aug 2020 14:19:02: #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 14:19:02: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:19:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:19:18: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:19:35: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:19:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:19:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.10_summits.bed INFO @ Mon, 10 Aug 2020 14:19:35: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (813 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:19:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:19:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:19:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047621/SRX8047621.20_summits.bed INFO @ Mon, 10 Aug 2020 14:19:51: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 2 millis CompletedMACS2peakCalling