Job ID = 8184181 SRX = SRX8047573 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T02:47:31 prefetch.2.10.7: 1) Downloading 'SRR11471298'... 2020-08-10T02:47:31 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T02:51:25 prefetch.2.10.7: HTTPS download succeed 2020-08-10T02:51:25 prefetch.2.10.7: 1) 'SRR11471298' was downloaded successfully Read 62575958 spots for SRR11471298/SRR11471298.sra Written 62575958 spots for SRR11471298/SRR11471298.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:38:47 62575958 reads; of these: 62575958 (100.00%) were unpaired; of these: 11355133 (18.15%) aligned 0 times 39970019 (63.87%) aligned exactly 1 time 11250806 (17.98%) aligned >1 times 81.85% overall alignment rate Time searching: 00:38:51 Overall time: 00:38:51 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 24 files... [bam_rmdupse_core] 6963263 / 51220825 = 0.1359 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 12:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.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 12:46:11: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:46:11: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:46:16: 1000000 INFO @ Mon, 10 Aug 2020 12:46:21: 2000000 INFO @ Mon, 10 Aug 2020 12:46:26: 3000000 INFO @ Mon, 10 Aug 2020 12:46:31: 4000000 INFO @ Mon, 10 Aug 2020 12:46:35: 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 12:46:40: 6000000 INFO @ Mon, 10 Aug 2020 12:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.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 12:46:41: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:46:41: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:46:45: 7000000 INFO @ Mon, 10 Aug 2020 12:46:46: 1000000 INFO @ Mon, 10 Aug 2020 12:46:50: 8000000 INFO @ Mon, 10 Aug 2020 12:46:51: 2000000 INFO @ Mon, 10 Aug 2020 12:46:55: 9000000 INFO @ Mon, 10 Aug 2020 12:46:56: 3000000 INFO @ Mon, 10 Aug 2020 12:47:00: 10000000 INFO @ Mon, 10 Aug 2020 12:47:01: 4000000 INFO @ Mon, 10 Aug 2020 12:47:05: 11000000 INFO @ Mon, 10 Aug 2020 12:47:06: 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 12:47:10: 12000000 INFO @ Mon, 10 Aug 2020 12:47:11: 6000000 INFO @ Mon, 10 Aug 2020 12:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.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 12:47:11: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:47:11: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:47:15: 13000000 INFO @ Mon, 10 Aug 2020 12:47:16: 7000000 INFO @ Mon, 10 Aug 2020 12:47:16: 1000000 INFO @ Mon, 10 Aug 2020 12:47:20: 14000000 INFO @ Mon, 10 Aug 2020 12:47:21: 8000000 INFO @ Mon, 10 Aug 2020 12:47:21: 2000000 INFO @ Mon, 10 Aug 2020 12:47:25: 15000000 INFO @ Mon, 10 Aug 2020 12:47:26: 9000000 INFO @ Mon, 10 Aug 2020 12:47:26: 3000000 INFO @ Mon, 10 Aug 2020 12:47:30: 16000000 INFO @ Mon, 10 Aug 2020 12:47:31: 10000000 INFO @ Mon, 10 Aug 2020 12:47:31: 4000000 INFO @ Mon, 10 Aug 2020 12:47:35: 17000000 INFO @ Mon, 10 Aug 2020 12:47:36: 11000000 INFO @ Mon, 10 Aug 2020 12:47:36: 5000000 INFO @ Mon, 10 Aug 2020 12:47:40: 18000000 INFO @ Mon, 10 Aug 2020 12:47:41: 12000000 INFO @ Mon, 10 Aug 2020 12:47:41: 6000000 INFO @ Mon, 10 Aug 2020 12:47:45: 19000000 INFO @ Mon, 10 Aug 2020 12:47:46: 13000000 INFO @ Mon, 10 Aug 2020 12:47:46: 7000000 INFO @ Mon, 10 Aug 2020 12:47:50: 20000000 INFO @ Mon, 10 Aug 2020 12:47:51: 14000000 INFO @ Mon, 10 Aug 2020 12:47:51: 8000000 INFO @ Mon, 10 Aug 2020 12:47:55: 21000000 INFO @ Mon, 10 Aug 2020 12:47:56: 15000000 INFO @ Mon, 10 Aug 2020 12:47:56: 9000000 INFO @ Mon, 10 Aug 2020 12:48:00: 22000000 INFO @ Mon, 10 Aug 2020 12:48:01: 16000000 INFO @ Mon, 10 Aug 2020 12:48:01: 10000000 INFO @ Mon, 10 Aug 2020 12:48:05: 23000000 INFO @ Mon, 10 Aug 2020 12:48:06: 17000000 INFO @ Mon, 10 Aug 2020 12:48:06: 11000000 INFO @ Mon, 10 Aug 2020 12:48:10: 24000000 INFO @ Mon, 10 Aug 2020 12:48:11: 18000000 INFO @ Mon, 10 Aug 2020 12:48:11: 12000000 INFO @ Mon, 10 Aug 2020 12:48:15: 25000000 INFO @ Mon, 10 Aug 2020 12:48:16: 19000000 INFO @ Mon, 10 Aug 2020 12:48:16: 13000000 INFO @ Mon, 10 Aug 2020 12:48:20: 26000000 INFO @ Mon, 10 Aug 2020 12:48:20: 20000000 INFO @ Mon, 10 Aug 2020 12:48:21: 14000000 INFO @ Mon, 10 Aug 2020 12:48:25: 27000000 INFO @ Mon, 10 Aug 2020 12:48:25: 21000000 INFO @ Mon, 10 Aug 2020 12:48:26: 15000000 INFO @ Mon, 10 Aug 2020 12:48:30: 28000000 INFO @ Mon, 10 Aug 2020 12:48:30: 22000000 INFO @ Mon, 10 Aug 2020 12:48:31: 16000000 INFO @ Mon, 10 Aug 2020 12:48:34: 29000000 INFO @ Mon, 10 Aug 2020 12:48:35: 23000000 INFO @ Mon, 10 Aug 2020 12:48:36: 17000000 INFO @ Mon, 10 Aug 2020 12:48:39: 30000000 INFO @ Mon, 10 Aug 2020 12:48:40: 24000000 INFO @ Mon, 10 Aug 2020 12:48:41: 18000000 INFO @ Mon, 10 Aug 2020 12:48:44: 31000000 INFO @ Mon, 10 Aug 2020 12:48:45: 25000000 INFO @ Mon, 10 Aug 2020 12:48:46: 19000000 INFO @ Mon, 10 Aug 2020 12:48:49: 32000000 INFO @ Mon, 10 Aug 2020 12:48:50: 26000000 INFO @ Mon, 10 Aug 2020 12:48:51: 20000000 INFO @ Mon, 10 Aug 2020 12:48:54: 33000000 INFO @ Mon, 10 Aug 2020 12:48:55: 27000000 INFO @ Mon, 10 Aug 2020 12:48:56: 21000000 INFO @ Mon, 10 Aug 2020 12:48:59: 34000000 INFO @ Mon, 10 Aug 2020 12:49:00: 28000000 INFO @ Mon, 10 Aug 2020 12:49:01: 22000000 INFO @ Mon, 10 Aug 2020 12:49:04: 35000000 INFO @ Mon, 10 Aug 2020 12:49:05: 29000000 INFO @ Mon, 10 Aug 2020 12:49:06: 23000000 INFO @ Mon, 10 Aug 2020 12:49:09: 36000000 INFO @ Mon, 10 Aug 2020 12:49:10: 30000000 INFO @ Mon, 10 Aug 2020 12:49:11: 24000000 INFO @ Mon, 10 Aug 2020 12:49:14: 37000000 INFO @ Mon, 10 Aug 2020 12:49:15: 31000000 INFO @ Mon, 10 Aug 2020 12:49:16: 25000000 INFO @ Mon, 10 Aug 2020 12:49:19: 38000000 INFO @ Mon, 10 Aug 2020 12:49:20: 32000000 INFO @ Mon, 10 Aug 2020 12:49:20: 26000000 INFO @ Mon, 10 Aug 2020 12:49:24: 39000000 INFO @ Mon, 10 Aug 2020 12:49:25: 33000000 INFO @ Mon, 10 Aug 2020 12:49:25: 27000000 INFO @ Mon, 10 Aug 2020 12:49:29: 40000000 INFO @ Mon, 10 Aug 2020 12:49:29: 34000000 INFO @ Mon, 10 Aug 2020 12:49:30: 28000000 INFO @ Mon, 10 Aug 2020 12:49:34: 41000000 INFO @ Mon, 10 Aug 2020 12:49:34: 35000000 INFO @ Mon, 10 Aug 2020 12:49:35: 29000000 INFO @ Mon, 10 Aug 2020 12:49:39: 42000000 INFO @ Mon, 10 Aug 2020 12:49:39: 36000000 INFO @ Mon, 10 Aug 2020 12:49:41: 30000000 INFO @ Mon, 10 Aug 2020 12:49:44: 37000000 INFO @ Mon, 10 Aug 2020 12:49:44: 43000000 INFO @ Mon, 10 Aug 2020 12:49:46: 31000000 INFO @ Mon, 10 Aug 2020 12:49:49: 38000000 INFO @ Mon, 10 Aug 2020 12:49:50: 44000000 INFO @ Mon, 10 Aug 2020 12:49:51: 32000000 INFO @ Mon, 10 Aug 2020 12:49:51: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:49:51: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:49:51: #1 total tags in treatment: 44257562 INFO @ Mon, 10 Aug 2020 12:49:51: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:49:51: #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 12:49:52: #1 tags after filtering in treatment: 44257480 INFO @ Mon, 10 Aug 2020 12:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:49:52: #1 finished! INFO @ Mon, 10 Aug 2020 12:49:52: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:49:54: 39000000 INFO @ Mon, 10 Aug 2020 12:49:56: 33000000 INFO @ Mon, 10 Aug 2020 12:49:57: #2 number of paired peaks: 42660 INFO @ Mon, 10 Aug 2020 12:49:57: start model_add_line... INFO @ Mon, 10 Aug 2020 12:49:57: start X-correlation... INFO @ Mon, 10 Aug 2020 12:49:57: end of X-cor INFO @ Mon, 10 Aug 2020 12:49:57: #2 finished! INFO @ Mon, 10 Aug 2020 12:49:57: #2 predicted fragment length is 121 bps INFO @ Mon, 10 Aug 2020 12:49:57: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 10 Aug 2020 12:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.05_model.r INFO @ Mon, 10 Aug 2020 12:49:57: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:49:59: 40000000 INFO @ Mon, 10 Aug 2020 12:50:01: 34000000 INFO @ Mon, 10 Aug 2020 12:50:05: 41000000 INFO @ Mon, 10 Aug 2020 12:50:07: 35000000 INFO @ Mon, 10 Aug 2020 12:50:10: 42000000 INFO @ Mon, 10 Aug 2020 12:50:12: 36000000 INFO @ Mon, 10 Aug 2020 12:50:15: 43000000 INFO @ Mon, 10 Aug 2020 12:50:17: 37000000 INFO @ Mon, 10 Aug 2020 12:50:20: 44000000 INFO @ Mon, 10 Aug 2020 12:50:21: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:50:21: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:50:21: #1 total tags in treatment: 44257562 INFO @ Mon, 10 Aug 2020 12:50:21: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:50:21: #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 12:50:22: 38000000 INFO @ Mon, 10 Aug 2020 12:50:22: #1 tags after filtering in treatment: 44257480 INFO @ Mon, 10 Aug 2020 12:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:50:22: #1 finished! INFO @ Mon, 10 Aug 2020 12:50:22: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:50:27: #2 number of paired peaks: 42660 INFO @ Mon, 10 Aug 2020 12:50:27: start model_add_line... INFO @ Mon, 10 Aug 2020 12:50:27: 39000000 INFO @ Mon, 10 Aug 2020 12:50:28: start X-correlation... INFO @ Mon, 10 Aug 2020 12:50:28: end of X-cor INFO @ Mon, 10 Aug 2020 12:50:28: #2 finished! INFO @ Mon, 10 Aug 2020 12:50:28: #2 predicted fragment length is 121 bps INFO @ Mon, 10 Aug 2020 12:50:28: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 10 Aug 2020 12:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.10_model.r INFO @ Mon, 10 Aug 2020 12:50:28: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:50:33: 40000000 INFO @ Mon, 10 Aug 2020 12:50:38: 41000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 12:50:43: 42000000 INFO @ Mon, 10 Aug 2020 12:50:48: 43000000 INFO @ Mon, 10 Aug 2020 12:50:53: 44000000 INFO @ Mon, 10 Aug 2020 12:50:54: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:50:54: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:50:54: #1 total tags in treatment: 44257562 INFO @ Mon, 10 Aug 2020 12:50:54: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:50:54: #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 12:50:55: #1 tags after filtering in treatment: 44257480 INFO @ Mon, 10 Aug 2020 12:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:50:55: #1 finished! INFO @ Mon, 10 Aug 2020 12:50:55: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:51:00: #2 number of paired peaks: 42660 INFO @ Mon, 10 Aug 2020 12:51:00: start model_add_line... INFO @ Mon, 10 Aug 2020 12:51:00: start X-correlation... INFO @ Mon, 10 Aug 2020 12:51:00: end of X-cor INFO @ Mon, 10 Aug 2020 12:51:00: #2 finished! INFO @ Mon, 10 Aug 2020 12:51:00: #2 predicted fragment length is 121 bps INFO @ Mon, 10 Aug 2020 12:51:00: #2 alternative fragment length(s) may be 121 bps INFO @ Mon, 10 Aug 2020 12:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.20_model.r INFO @ Mon, 10 Aug 2020 12:51:00: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:51:38: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:52:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 12:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.05_peaks.xls INFO @ Mon, 10 Aug 2020 12:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.05_summits.bed INFO @ Mon, 10 Aug 2020 12:52:33: Done! pass1 - making usageList (118 chroms): 4 millis pass2 - checking and writing primary data (30044 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:52:40: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.10_peaks.xls INFO @ Mon, 10 Aug 2020 12:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:52:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.10_summits.bed INFO @ Mon, 10 Aug 2020 12:52:57: Done! pass1 - making usageList (92 chroms): 4 millis pass2 - checking and writing primary data (18117 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.20_peaks.xls INFO @ Mon, 10 Aug 2020 12:53:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:53:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047573/SRX8047573.20_summits.bed INFO @ Mon, 10 Aug 2020 12:53:35: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (10095 records, 4 fields): 11 millis CompletedMACS2peakCalling