Job ID = 8184305 SRX = SRX8047583 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:10:46 prefetch.2.10.7: 1) Downloading 'SRR11471308'... 2020-08-10T03:10:46 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:13:08 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:13:08 prefetch.2.10.7: 1) 'SRR11471308' was downloaded successfully Read 62885475 spots for SRR11471308/SRR11471308.sra Written 62885475 spots for SRR11471308/SRR11471308.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: 00:00:00 Multiseed full-index search: 00:32:57 62885475 reads; of these: 62885475 (100.00%) were unpaired; of these: 2578216 (4.10%) aligned 0 times 49738513 (79.09%) aligned exactly 1 time 10568746 (16.81%) aligned >1 times 95.90% overall alignment rate Time searching: 00:32:58 Overall time: 00:32:58 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 28 files... [bam_rmdupse_core] 16232602 / 60307259 = 0.2692 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 13:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.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 13:04:01: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:04:01: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:04:08: 1000000 INFO @ Mon, 10 Aug 2020 13:04:14: 2000000 INFO @ Mon, 10 Aug 2020 13:04:20: 3000000 INFO @ Mon, 10 Aug 2020 13:04:27: 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 @ Mon, 10 Aug 2020 13:04:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.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 13:04:31: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:04:31: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:04:33: 5000000 INFO @ Mon, 10 Aug 2020 13:04:38: 1000000 INFO @ Mon, 10 Aug 2020 13:04:39: 6000000 INFO @ Mon, 10 Aug 2020 13:04:44: 2000000 INFO @ Mon, 10 Aug 2020 13:04:46: 7000000 INFO @ Mon, 10 Aug 2020 13:04:51: 3000000 INFO @ Mon, 10 Aug 2020 13:04:52: 8000000 INFO @ Mon, 10 Aug 2020 13:04:57: 4000000 INFO @ Mon, 10 Aug 2020 13:04:59: 9000000 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 13:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.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 13:05:01: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:05:01: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:05:04: 5000000 INFO @ Mon, 10 Aug 2020 13:05:06: 10000000 INFO @ Mon, 10 Aug 2020 13:05:08: 1000000 INFO @ Mon, 10 Aug 2020 13:05:10: 6000000 INFO @ Mon, 10 Aug 2020 13:05:13: 11000000 INFO @ Mon, 10 Aug 2020 13:05:15: 2000000 INFO @ Mon, 10 Aug 2020 13:05:17: 7000000 INFO @ Mon, 10 Aug 2020 13:05:20: 12000000 INFO @ Mon, 10 Aug 2020 13:05:22: 3000000 INFO @ Mon, 10 Aug 2020 13:05:24: 8000000 INFO @ Mon, 10 Aug 2020 13:05:27: 13000000 INFO @ Mon, 10 Aug 2020 13:05:28: 4000000 INFO @ Mon, 10 Aug 2020 13:05:30: 9000000 INFO @ Mon, 10 Aug 2020 13:05:34: 14000000 INFO @ Mon, 10 Aug 2020 13:05:35: 5000000 INFO @ Mon, 10 Aug 2020 13:05:37: 10000000 INFO @ Mon, 10 Aug 2020 13:05:41: 15000000 INFO @ Mon, 10 Aug 2020 13:05:41: 6000000 INFO @ Mon, 10 Aug 2020 13:05:44: 11000000 INFO @ Mon, 10 Aug 2020 13:05:48: 7000000 INFO @ Mon, 10 Aug 2020 13:05:48: 16000000 INFO @ Mon, 10 Aug 2020 13:05:51: 12000000 INFO @ Mon, 10 Aug 2020 13:05:55: 8000000 INFO @ Mon, 10 Aug 2020 13:05:55: 17000000 INFO @ Mon, 10 Aug 2020 13:05:58: 13000000 INFO @ Mon, 10 Aug 2020 13:06:01: 9000000 INFO @ Mon, 10 Aug 2020 13:06:02: 18000000 INFO @ Mon, 10 Aug 2020 13:06:05: 14000000 INFO @ Mon, 10 Aug 2020 13:06:08: 10000000 INFO @ Mon, 10 Aug 2020 13:06:09: 19000000 INFO @ Mon, 10 Aug 2020 13:06:12: 15000000 INFO @ Mon, 10 Aug 2020 13:06:16: 11000000 INFO @ Mon, 10 Aug 2020 13:06:16: 20000000 INFO @ Mon, 10 Aug 2020 13:06:19: 16000000 INFO @ Mon, 10 Aug 2020 13:06:23: 12000000 INFO @ Mon, 10 Aug 2020 13:06:23: 21000000 INFO @ Mon, 10 Aug 2020 13:06:26: 17000000 INFO @ Mon, 10 Aug 2020 13:06:30: 13000000 INFO @ Mon, 10 Aug 2020 13:06:31: 22000000 INFO @ Mon, 10 Aug 2020 13:06:33: 18000000 INFO @ Mon, 10 Aug 2020 13:06:37: 14000000 INFO @ Mon, 10 Aug 2020 13:06:38: 23000000 INFO @ Mon, 10 Aug 2020 13:06:40: 19000000 INFO @ Mon, 10 Aug 2020 13:06:44: 15000000 INFO @ Mon, 10 Aug 2020 13:06:45: 24000000 INFO @ Mon, 10 Aug 2020 13:06:47: 20000000 INFO @ Mon, 10 Aug 2020 13:06:51: 16000000 INFO @ Mon, 10 Aug 2020 13:06:52: 25000000 INFO @ Mon, 10 Aug 2020 13:06:54: 21000000 INFO @ Mon, 10 Aug 2020 13:06:58: 17000000 INFO @ Mon, 10 Aug 2020 13:06:59: 26000000 INFO @ Mon, 10 Aug 2020 13:07:01: 22000000 INFO @ Mon, 10 Aug 2020 13:07:05: 18000000 INFO @ Mon, 10 Aug 2020 13:07:06: 27000000 INFO @ Mon, 10 Aug 2020 13:07:07: 23000000 INFO @ Mon, 10 Aug 2020 13:07:11: 19000000 INFO @ Mon, 10 Aug 2020 13:07:13: 28000000 INFO @ Mon, 10 Aug 2020 13:07:14: 24000000 INFO @ Mon, 10 Aug 2020 13:07:18: 20000000 INFO @ Mon, 10 Aug 2020 13:07:20: 29000000 INFO @ Mon, 10 Aug 2020 13:07:21: 25000000 INFO @ Mon, 10 Aug 2020 13:07:25: 21000000 INFO @ Mon, 10 Aug 2020 13:07:27: 30000000 INFO @ Mon, 10 Aug 2020 13:07:27: 26000000 INFO @ Mon, 10 Aug 2020 13:07:32: 22000000 INFO @ Mon, 10 Aug 2020 13:07:34: 27000000 INFO @ Mon, 10 Aug 2020 13:07:34: 31000000 INFO @ Mon, 10 Aug 2020 13:07:38: 23000000 INFO @ Mon, 10 Aug 2020 13:07:41: 28000000 INFO @ Mon, 10 Aug 2020 13:07:41: 32000000 INFO @ Mon, 10 Aug 2020 13:07:45: 24000000 INFO @ Mon, 10 Aug 2020 13:07:48: 29000000 INFO @ Mon, 10 Aug 2020 13:07:48: 33000000 INFO @ Mon, 10 Aug 2020 13:07:52: 25000000 INFO @ Mon, 10 Aug 2020 13:07:54: 30000000 INFO @ Mon, 10 Aug 2020 13:07:55: 34000000 INFO @ Mon, 10 Aug 2020 13:07:58: 26000000 INFO @ Mon, 10 Aug 2020 13:08:01: 31000000 INFO @ Mon, 10 Aug 2020 13:08:02: 35000000 INFO @ Mon, 10 Aug 2020 13:08:05: 27000000 INFO @ Mon, 10 Aug 2020 13:08:08: 32000000 INFO @ Mon, 10 Aug 2020 13:08:09: 36000000 INFO @ Mon, 10 Aug 2020 13:08:11: 28000000 INFO @ Mon, 10 Aug 2020 13:08:15: 33000000 INFO @ Mon, 10 Aug 2020 13:08:16: 37000000 INFO @ Mon, 10 Aug 2020 13:08:18: 29000000 INFO @ Mon, 10 Aug 2020 13:08:21: 34000000 INFO @ Mon, 10 Aug 2020 13:08:23: 38000000 INFO @ Mon, 10 Aug 2020 13:08:25: 30000000 INFO @ Mon, 10 Aug 2020 13:08:28: 35000000 INFO @ Mon, 10 Aug 2020 13:08:30: 39000000 INFO @ Mon, 10 Aug 2020 13:08:32: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:08:35: 36000000 INFO @ Mon, 10 Aug 2020 13:08:37: 40000000 INFO @ Mon, 10 Aug 2020 13:08:38: 32000000 INFO @ Mon, 10 Aug 2020 13:08:41: 37000000 INFO @ Mon, 10 Aug 2020 13:08:44: 41000000 INFO @ Mon, 10 Aug 2020 13:08:45: 33000000 INFO @ Mon, 10 Aug 2020 13:08:48: 38000000 INFO @ Mon, 10 Aug 2020 13:08:51: 42000000 INFO @ Mon, 10 Aug 2020 13:08:52: 34000000 INFO @ Mon, 10 Aug 2020 13:08:55: 39000000 INFO @ Mon, 10 Aug 2020 13:08:58: 35000000 INFO @ Mon, 10 Aug 2020 13:08:58: 43000000 INFO @ Mon, 10 Aug 2020 13:09:01: 40000000 INFO @ Mon, 10 Aug 2020 13:09:05: 36000000 INFO @ Mon, 10 Aug 2020 13:09:05: 44000000 INFO @ Mon, 10 Aug 2020 13:09:06: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:09:06: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:09:06: #1 total tags in treatment: 44074657 INFO @ Mon, 10 Aug 2020 13:09:06: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:09:06: #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 13:09:07: #1 tags after filtering in treatment: 44074558 INFO @ Mon, 10 Aug 2020 13:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:09:07: #1 finished! INFO @ Mon, 10 Aug 2020 13:09:07: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:09:08: 41000000 INFO @ Mon, 10 Aug 2020 13:09:12: 37000000 INFO @ Mon, 10 Aug 2020 13:09:14: #2 number of paired peaks: 54168 INFO @ Mon, 10 Aug 2020 13:09:14: start model_add_line... INFO @ Mon, 10 Aug 2020 13:09:14: start X-correlation... INFO @ Mon, 10 Aug 2020 13:09:14: end of X-cor INFO @ Mon, 10 Aug 2020 13:09:14: #2 finished! INFO @ Mon, 10 Aug 2020 13:09:14: #2 predicted fragment length is 124 bps INFO @ Mon, 10 Aug 2020 13:09:14: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 10 Aug 2020 13:09:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.05_model.r INFO @ Mon, 10 Aug 2020 13:09:14: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:09:15: 42000000 INFO @ Mon, 10 Aug 2020 13:09:18: 38000000 INFO @ Mon, 10 Aug 2020 13:09:21: 43000000 INFO @ Mon, 10 Aug 2020 13:09:25: 39000000 INFO @ Mon, 10 Aug 2020 13:09:28: 44000000 INFO @ Mon, 10 Aug 2020 13:09:29: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:09:29: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:09:29: #1 total tags in treatment: 44074657 INFO @ Mon, 10 Aug 2020 13:09:29: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:09:29: #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 13:09:30: #1 tags after filtering in treatment: 44074558 INFO @ Mon, 10 Aug 2020 13:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:09:30: #1 finished! INFO @ Mon, 10 Aug 2020 13:09:30: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:09:31: 40000000 INFO @ Mon, 10 Aug 2020 13:09:36: #2 number of paired peaks: 54168 INFO @ Mon, 10 Aug 2020 13:09:36: start model_add_line... INFO @ Mon, 10 Aug 2020 13:09:37: start X-correlation... INFO @ Mon, 10 Aug 2020 13:09:37: end of X-cor INFO @ Mon, 10 Aug 2020 13:09:37: #2 finished! INFO @ Mon, 10 Aug 2020 13:09:37: #2 predicted fragment length is 124 bps INFO @ Mon, 10 Aug 2020 13:09:37: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 10 Aug 2020 13:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.10_model.r INFO @ Mon, 10 Aug 2020 13:09:37: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:09:38: 41000000 INFO @ Mon, 10 Aug 2020 13:09:44: 42000000 INFO @ Mon, 10 Aug 2020 13:09:51: 43000000 INFO @ Mon, 10 Aug 2020 13:09:57: 44000000 BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:09:58: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:09:58: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:09:58: #1 total tags in treatment: 44074657 INFO @ Mon, 10 Aug 2020 13:09:58: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:09:58: #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 13:09:59: #1 tags after filtering in treatment: 44074558 INFO @ Mon, 10 Aug 2020 13:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:09:59: #1 finished! INFO @ Mon, 10 Aug 2020 13:09:59: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:10:05: #2 number of paired peaks: 54168 INFO @ Mon, 10 Aug 2020 13:10:05: start model_add_line... INFO @ Mon, 10 Aug 2020 13:10:06: start X-correlation... INFO @ Mon, 10 Aug 2020 13:10:06: end of X-cor INFO @ Mon, 10 Aug 2020 13:10:06: #2 finished! INFO @ Mon, 10 Aug 2020 13:10:06: #2 predicted fragment length is 124 bps INFO @ Mon, 10 Aug 2020 13:10:06: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 10 Aug 2020 13:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.20_model.r INFO @ Mon, 10 Aug 2020 13:10:06: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:11:08: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:11:25: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:11:47: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.05_summits.bed INFO @ Mon, 10 Aug 2020 13:12:08: Done! pass1 - making usageList (144 chroms): 7 millis pass2 - checking and writing primary data (37452 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.10_summits.bed INFO @ Mon, 10 Aug 2020 13:12:23: Done! pass1 - making usageList (130 chroms): 5 millis pass2 - checking and writing primary data (31419 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:12:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047583/SRX8047583.20_summits.bed INFO @ Mon, 10 Aug 2020 13:12:42: Done! pass1 - making usageList (103 chroms): 4 millis pass2 - checking and writing primary data (25265 records, 4 fields): 28 millis CompletedMACS2peakCalling