Job ID = 8184599 SRX = SRX8047616 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:50:19 prefetch.2.10.7: 1) Downloading 'SRR11471340'... 2020-08-10T04:50:19 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:54:26 prefetch.2.10.7: HTTPS download failed 2020-08-10T04:54:26 prefetch.2.10.7: 1) failed to download SRR11471340 2020-08-10T04:54:36 prefetch.2.10.7: 1) Downloading 'SRR11471340'... 2020-08-10T04:54:36 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:54:36 prefetch.2.10.7: Continue download of 'SRR11471340' from 1432360677 2020-08-10T04:54:44 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:54:44 prefetch.2.10.7: 1) 'SRR11471340' was downloaded successfully Read 40100915 spots for SRR11471340/SRR11471340.sra Written 40100915 spots for SRR11471340/SRR11471340.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: 01:27:40 40100915 reads; of these: 40100915 (100.00%) were unpaired; of these: 3103599 (7.74%) aligned 0 times 16834513 (41.98%) aligned exactly 1 time 20162803 (50.28%) aligned >1 times 92.26% overall alignment rate Time searching: 01:27:42 Overall time: 01:27:42 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 16 files... [bam_rmdupse_core] 4060066 / 36997316 = 0.1097 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 15:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.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 15:34:07: #1 read tag files... INFO @ Mon, 10 Aug 2020 15:34:07: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 15:34:12: 1000000 INFO @ Mon, 10 Aug 2020 15:34:18: 2000000 INFO @ Mon, 10 Aug 2020 15:34:23: 3000000 INFO @ Mon, 10 Aug 2020 15:34:29: 4000000 INFO @ Mon, 10 Aug 2020 15:34:35: 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 15:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.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 15:34:36: #1 read tag files... INFO @ Mon, 10 Aug 2020 15:34:36: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 15:34:40: 6000000 INFO @ Mon, 10 Aug 2020 15:34:43: 1000000 INFO @ Mon, 10 Aug 2020 15:34:47: 7000000 INFO @ Mon, 10 Aug 2020 15:34:49: 2000000 INFO @ Mon, 10 Aug 2020 15:34:53: 8000000 INFO @ Mon, 10 Aug 2020 15:34:55: 3000000 INFO @ Mon, 10 Aug 2020 15:34:59: 9000000 INFO @ Mon, 10 Aug 2020 15:35:01: 4000000 BedGraph に変換中... INFO @ Mon, 10 Aug 2020 15:35:05: 10000000 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 15:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.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 15:35:07: #1 read tag files... INFO @ Mon, 10 Aug 2020 15:35:07: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 15:35:07: 5000000 INFO @ Mon, 10 Aug 2020 15:35:11: 11000000 INFO @ Mon, 10 Aug 2020 15:35:13: 6000000 INFO @ Mon, 10 Aug 2020 15:35:14: 1000000 INFO @ Mon, 10 Aug 2020 15:35:18: 12000000 INFO @ Mon, 10 Aug 2020 15:35:20: 7000000 INFO @ Mon, 10 Aug 2020 15:35:21: 2000000 INFO @ Mon, 10 Aug 2020 15:35:24: 13000000 INFO @ Mon, 10 Aug 2020 15:35:26: 8000000 INFO @ Mon, 10 Aug 2020 15:35:28: 3000000 INFO @ Mon, 10 Aug 2020 15:35:31: 14000000 INFO @ Mon, 10 Aug 2020 15:35:33: 9000000 INFO @ Mon, 10 Aug 2020 15:35:35: 4000000 INFO @ Mon, 10 Aug 2020 15:35:37: 15000000 INFO @ Mon, 10 Aug 2020 15:35:39: 10000000 INFO @ Mon, 10 Aug 2020 15:35:41: 5000000 INFO @ Mon, 10 Aug 2020 15:35:43: 16000000 INFO @ Mon, 10 Aug 2020 15:35:45: 11000000 INFO @ Mon, 10 Aug 2020 15:35:48: 6000000 INFO @ Mon, 10 Aug 2020 15:35:50: 17000000 INFO @ Mon, 10 Aug 2020 15:35:52: 12000000 INFO @ Mon, 10 Aug 2020 15:35:55: 7000000 INFO @ Mon, 10 Aug 2020 15:35:56: 18000000 INFO @ Mon, 10 Aug 2020 15:35:58: 13000000 INFO @ Mon, 10 Aug 2020 15:36:02: 8000000 INFO @ Mon, 10 Aug 2020 15:36:02: 19000000 INFO @ Mon, 10 Aug 2020 15:36:04: 14000000 INFO @ Mon, 10 Aug 2020 15:36:08: 9000000 INFO @ Mon, 10 Aug 2020 15:36:08: 20000000 INFO @ Mon, 10 Aug 2020 15:36:10: 15000000 INFO @ Mon, 10 Aug 2020 15:36:14: 21000000 INFO @ Mon, 10 Aug 2020 15:36:15: 10000000 INFO @ Mon, 10 Aug 2020 15:36:17: 16000000 INFO @ Mon, 10 Aug 2020 15:36:21: 22000000 INFO @ Mon, 10 Aug 2020 15:36:21: 11000000 INFO @ Mon, 10 Aug 2020 15:36:23: 17000000 INFO @ Mon, 10 Aug 2020 15:36:27: 23000000 INFO @ Mon, 10 Aug 2020 15:36:28: 12000000 INFO @ Mon, 10 Aug 2020 15:36:29: 18000000 INFO @ Mon, 10 Aug 2020 15:36:33: 24000000 INFO @ Mon, 10 Aug 2020 15:36:35: 13000000 INFO @ Mon, 10 Aug 2020 15:36:35: 19000000 INFO @ Mon, 10 Aug 2020 15:36:39: 25000000 INFO @ Mon, 10 Aug 2020 15:36:41: 14000000 INFO @ Mon, 10 Aug 2020 15:36:41: 20000000 INFO @ Mon, 10 Aug 2020 15:36:45: 26000000 INFO @ Mon, 10 Aug 2020 15:36:48: 21000000 INFO @ Mon, 10 Aug 2020 15:36:48: 15000000 INFO @ Mon, 10 Aug 2020 15:36:51: 27000000 INFO @ Mon, 10 Aug 2020 15:36:54: 22000000 INFO @ Mon, 10 Aug 2020 15:36:55: 16000000 INFO @ Mon, 10 Aug 2020 15:36:57: 28000000 INFO @ Mon, 10 Aug 2020 15:37:00: 23000000 INFO @ Mon, 10 Aug 2020 15:37:01: 17000000 INFO @ Mon, 10 Aug 2020 15:37:04: 29000000 INFO @ Mon, 10 Aug 2020 15:37:07: 24000000 INFO @ Mon, 10 Aug 2020 15:37:08: 18000000 INFO @ Mon, 10 Aug 2020 15:37:10: 30000000 INFO @ Mon, 10 Aug 2020 15:37:13: 25000000 INFO @ Mon, 10 Aug 2020 15:37:15: 19000000 INFO @ Mon, 10 Aug 2020 15:37:16: 31000000 INFO @ Mon, 10 Aug 2020 15:37:20: 26000000 INFO @ Mon, 10 Aug 2020 15:37:22: 20000000 INFO @ Mon, 10 Aug 2020 15:37:23: 32000000 INFO @ Mon, 10 Aug 2020 15:37:26: 27000000 INFO @ Mon, 10 Aug 2020 15:37:29: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 15:37:29: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 15:37:29: #1 total tags in treatment: 32937250 INFO @ Mon, 10 Aug 2020 15:37:29: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 15:37:29: #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 15:37:29: 21000000 INFO @ Mon, 10 Aug 2020 15:37:29: #1 tags after filtering in treatment: 32937166 INFO @ Mon, 10 Aug 2020 15:37:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 15:37:29: #1 finished! INFO @ Mon, 10 Aug 2020 15:37:29: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 15:37:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 15:37:32: 28000000 INFO @ Mon, 10 Aug 2020 15:37:33: #2 number of paired peaks: 38235 INFO @ Mon, 10 Aug 2020 15:37:33: start model_add_line... INFO @ Mon, 10 Aug 2020 15:37:34: start X-correlation... INFO @ Mon, 10 Aug 2020 15:37:34: end of X-cor INFO @ Mon, 10 Aug 2020 15:37:34: #2 finished! INFO @ Mon, 10 Aug 2020 15:37:34: #2 predicted fragment length is 61 bps INFO @ Mon, 10 Aug 2020 15:37:34: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 10 Aug 2020 15:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.05_model.r WARNING @ Mon, 10 Aug 2020 15:37:34: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 15:37:34: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 10 Aug 2020 15:37:34: #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 15:37:34: #3 Call peaks... INFO @ Mon, 10 Aug 2020 15:37:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 15:37:36: 22000000 INFO @ Mon, 10 Aug 2020 15:37:39: 29000000 INFO @ Mon, 10 Aug 2020 15:37:42: 23000000 INFO @ Mon, 10 Aug 2020 15:37:45: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 15:37:49: 24000000 INFO @ Mon, 10 Aug 2020 15:37:51: 31000000 INFO @ Mon, 10 Aug 2020 15:37:55: 25000000 INFO @ Mon, 10 Aug 2020 15:37:58: 32000000 INFO @ Mon, 10 Aug 2020 15:38:01: 26000000 INFO @ Mon, 10 Aug 2020 15:38:04: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 15:38:04: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 15:38:04: #1 total tags in treatment: 32937250 INFO @ Mon, 10 Aug 2020 15:38:04: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 15:38:04: #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 15:38:04: #1 tags after filtering in treatment: 32937166 INFO @ Mon, 10 Aug 2020 15:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 15:38:04: #1 finished! INFO @ Mon, 10 Aug 2020 15:38:04: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 15:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 15:38:08: 27000000 INFO @ Mon, 10 Aug 2020 15:38:08: #2 number of paired peaks: 38235 INFO @ Mon, 10 Aug 2020 15:38:08: start model_add_line... INFO @ Mon, 10 Aug 2020 15:38:09: start X-correlation... INFO @ Mon, 10 Aug 2020 15:38:09: end of X-cor INFO @ Mon, 10 Aug 2020 15:38:09: #2 finished! INFO @ Mon, 10 Aug 2020 15:38:09: #2 predicted fragment length is 61 bps INFO @ Mon, 10 Aug 2020 15:38:09: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 10 Aug 2020 15:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.10_model.r WARNING @ Mon, 10 Aug 2020 15:38:09: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 15:38:09: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 10 Aug 2020 15:38:09: #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 15:38:09: #3 Call peaks... INFO @ Mon, 10 Aug 2020 15:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 15:38:14: 28000000 INFO @ Mon, 10 Aug 2020 15:38:19: 29000000 INFO @ Mon, 10 Aug 2020 15:38:25: 30000000 INFO @ Mon, 10 Aug 2020 15:38:31: 31000000 INFO @ Mon, 10 Aug 2020 15:38:37: 32000000 INFO @ Mon, 10 Aug 2020 15:38:42: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 15:38:42: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 15:38:42: #1 total tags in treatment: 32937250 INFO @ Mon, 10 Aug 2020 15:38:42: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 15:38:42: #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 15:38:43: #1 tags after filtering in treatment: 32937166 INFO @ Mon, 10 Aug 2020 15:38:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 15:38:43: #1 finished! INFO @ Mon, 10 Aug 2020 15:38:43: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 15:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 15:38:43: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 15:38:47: #2 number of paired peaks: 38235 INFO @ Mon, 10 Aug 2020 15:38:47: start model_add_line... INFO @ Mon, 10 Aug 2020 15:38:47: start X-correlation... INFO @ Mon, 10 Aug 2020 15:38:47: end of X-cor INFO @ Mon, 10 Aug 2020 15:38:47: #2 finished! INFO @ Mon, 10 Aug 2020 15:38:47: #2 predicted fragment length is 61 bps INFO @ Mon, 10 Aug 2020 15:38:47: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 10 Aug 2020 15:38:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.20_model.r WARNING @ Mon, 10 Aug 2020 15:38:47: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 15:38:47: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 10 Aug 2020 15:38:47: #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 15:38:47: #3 Call peaks... INFO @ Mon, 10 Aug 2020 15:38:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 15:39:18: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 15:39:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.05_peaks.xls INFO @ Mon, 10 Aug 2020 15:39:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 15:39:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.05_summits.bed INFO @ Mon, 10 Aug 2020 15:39:21: Done! pass1 - making usageList (176 chroms): 6 millis pass2 - checking and writing primary data (39419 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 15:39:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.10_peaks.xls INFO @ Mon, 10 Aug 2020 15:39:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 15:39:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.10_summits.bed INFO @ Mon, 10 Aug 2020 15:39:55: Done! pass1 - making usageList (92 chroms): 2 millis pass2 - checking and writing primary data (11699 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 15:39:58: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 15:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.20_peaks.xls INFO @ Mon, 10 Aug 2020 15:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 15:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047616/SRX8047616.20_summits.bed INFO @ Mon, 10 Aug 2020 15:40:34: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (2610 records, 4 fields): 7 millis CompletedMACS2peakCalling