Job ID = 10223642 SRX = ERX2745121 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T19:46:47 prefetch.2.10.7: 1) Downloading 'ERR2731896'... 2020-10-15T19:46:47 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T19:48:35 prefetch.2.10.7: HTTPS download succeed 2020-10-15T19:48:35 prefetch.2.10.7: 1) 'ERR2731896' was downloaded successfully Read 87739699 spots for ERR2731896/ERR2731896.sra Written 87739699 spots for ERR2731896/ERR2731896.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:41:16 87739699 reads; of these: 87739699 (100.00%) were unpaired; of these: 3338263 (3.80%) aligned 0 times 72126486 (82.21%) aligned exactly 1 time 12274950 (13.99%) aligned >1 times 96.20% overall alignment rate Time searching: 00:41:19 Overall time: 00:41:19 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 36 files... [bam_rmdupse_core] 46489249 / 84401436 = 0.5508 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 @ Fri, 16 Oct 2020 05:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.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 @ Fri, 16 Oct 2020 05:45:04: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:45:04: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:45:09: 1000000 INFO @ Fri, 16 Oct 2020 05:45:15: 2000000 INFO @ Fri, 16 Oct 2020 05:45:20: 3000000 INFO @ Fri, 16 Oct 2020 05:45:25: 4000000 INFO @ Fri, 16 Oct 2020 05:45:30: 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 @ Fri, 16 Oct 2020 05:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.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 @ Fri, 16 Oct 2020 05:45:33: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:45:33: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:45:36: 6000000 INFO @ Fri, 16 Oct 2020 05:45:40: 1000000 INFO @ Fri, 16 Oct 2020 05:45:42: 7000000 INFO @ Fri, 16 Oct 2020 05:45:47: 2000000 INFO @ Fri, 16 Oct 2020 05:45:48: 8000000 INFO @ Fri, 16 Oct 2020 05:45:54: 9000000 INFO @ Fri, 16 Oct 2020 05:45:54: 3000000 INFO @ Fri, 16 Oct 2020 05:46:00: 10000000 INFO @ Fri, 16 Oct 2020 05:46:01: 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 @ Fri, 16 Oct 2020 05:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.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 @ Fri, 16 Oct 2020 05:46:03: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:46:03: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:46:06: 11000000 INFO @ Fri, 16 Oct 2020 05:46:08: 5000000 INFO @ Fri, 16 Oct 2020 05:46:10: 1000000 INFO @ Fri, 16 Oct 2020 05:46:13: 12000000 INFO @ Fri, 16 Oct 2020 05:46:15: 6000000 INFO @ Fri, 16 Oct 2020 05:46:17: 2000000 INFO @ Fri, 16 Oct 2020 05:46:19: 13000000 INFO @ Fri, 16 Oct 2020 05:46:22: 7000000 INFO @ Fri, 16 Oct 2020 05:46:24: 3000000 INFO @ Fri, 16 Oct 2020 05:46:25: 14000000 INFO @ Fri, 16 Oct 2020 05:46:30: 8000000 INFO @ Fri, 16 Oct 2020 05:46:30: 4000000 INFO @ Fri, 16 Oct 2020 05:46:31: 15000000 INFO @ Fri, 16 Oct 2020 05:46:37: 9000000 INFO @ Fri, 16 Oct 2020 05:46:37: 16000000 INFO @ Fri, 16 Oct 2020 05:46:37: 5000000 INFO @ Fri, 16 Oct 2020 05:46:43: 17000000 INFO @ Fri, 16 Oct 2020 05:46:44: 10000000 INFO @ Fri, 16 Oct 2020 05:46:44: 6000000 INFO @ Fri, 16 Oct 2020 05:46:50: 18000000 INFO @ Fri, 16 Oct 2020 05:46:51: 7000000 INFO @ Fri, 16 Oct 2020 05:46:51: 11000000 INFO @ Fri, 16 Oct 2020 05:46:56: 19000000 INFO @ Fri, 16 Oct 2020 05:46:57: 8000000 INFO @ Fri, 16 Oct 2020 05:46:57: 12000000 INFO @ Fri, 16 Oct 2020 05:47:02: 20000000 INFO @ Fri, 16 Oct 2020 05:47:04: 9000000 INFO @ Fri, 16 Oct 2020 05:47:04: 13000000 INFO @ Fri, 16 Oct 2020 05:47:08: 21000000 INFO @ Fri, 16 Oct 2020 05:47:11: 14000000 INFO @ Fri, 16 Oct 2020 05:47:11: 10000000 INFO @ Fri, 16 Oct 2020 05:47:14: 22000000 INFO @ Fri, 16 Oct 2020 05:47:18: 15000000 INFO @ Fri, 16 Oct 2020 05:47:18: 11000000 INFO @ Fri, 16 Oct 2020 05:47:21: 23000000 INFO @ Fri, 16 Oct 2020 05:47:24: 16000000 INFO @ Fri, 16 Oct 2020 05:47:24: 12000000 INFO @ Fri, 16 Oct 2020 05:47:27: 24000000 INFO @ Fri, 16 Oct 2020 05:47:31: 17000000 INFO @ Fri, 16 Oct 2020 05:47:31: 13000000 INFO @ Fri, 16 Oct 2020 05:47:33: 25000000 INFO @ Fri, 16 Oct 2020 05:47:38: 18000000 INFO @ Fri, 16 Oct 2020 05:47:38: 14000000 INFO @ Fri, 16 Oct 2020 05:47:39: 26000000 INFO @ Fri, 16 Oct 2020 05:47:45: 19000000 INFO @ Fri, 16 Oct 2020 05:47:45: 15000000 INFO @ Fri, 16 Oct 2020 05:47:45: 27000000 INFO @ Fri, 16 Oct 2020 05:47:51: 28000000 INFO @ Fri, 16 Oct 2020 05:47:52: 20000000 INFO @ Fri, 16 Oct 2020 05:47:52: 16000000 INFO @ Fri, 16 Oct 2020 05:47:58: 29000000 INFO @ Fri, 16 Oct 2020 05:47:59: 21000000 INFO @ Fri, 16 Oct 2020 05:47:59: 17000000 INFO @ Fri, 16 Oct 2020 05:48:04: 30000000 INFO @ Fri, 16 Oct 2020 05:48:06: 22000000 INFO @ Fri, 16 Oct 2020 05:48:06: 18000000 INFO @ Fri, 16 Oct 2020 05:48:10: 31000000 INFO @ Fri, 16 Oct 2020 05:48:12: 23000000 INFO @ Fri, 16 Oct 2020 05:48:13: 19000000 INFO @ Fri, 16 Oct 2020 05:48:16: 32000000 INFO @ Fri, 16 Oct 2020 05:48:19: 24000000 INFO @ Fri, 16 Oct 2020 05:48:19: 20000000 INFO @ Fri, 16 Oct 2020 05:48:23: 33000000 INFO @ Fri, 16 Oct 2020 05:48:26: 25000000 INFO @ Fri, 16 Oct 2020 05:48:26: 21000000 INFO @ Fri, 16 Oct 2020 05:48:29: 34000000 INFO @ Fri, 16 Oct 2020 05:48:32: 26000000 INFO @ Fri, 16 Oct 2020 05:48:33: 22000000 INFO @ Fri, 16 Oct 2020 05:48:35: 35000000 INFO @ Fri, 16 Oct 2020 05:48:39: 27000000 INFO @ Fri, 16 Oct 2020 05:48:40: 23000000 INFO @ Fri, 16 Oct 2020 05:48:41: 36000000 INFO @ Fri, 16 Oct 2020 05:48:46: 28000000 INFO @ Fri, 16 Oct 2020 05:48:47: 24000000 INFO @ Fri, 16 Oct 2020 05:48:48: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 05:48:53: 29000000 INFO @ Fri, 16 Oct 2020 05:48:54: 25000000 INFO @ Fri, 16 Oct 2020 05:48:54: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:48:54: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:48:54: #1 total tags in treatment: 37912187 INFO @ Fri, 16 Oct 2020 05:48:54: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:48:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:48:55: #1 tags after filtering in treatment: 37912066 INFO @ Fri, 16 Oct 2020 05:48:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:48:55: #1 finished! INFO @ Fri, 16 Oct 2020 05:48:55: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:48:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:48:59: #2 number of paired peaks: 34889 INFO @ Fri, 16 Oct 2020 05:48:59: start model_add_line... INFO @ Fri, 16 Oct 2020 05:48:59: 30000000 INFO @ Fri, 16 Oct 2020 05:49:00: start X-correlation... INFO @ Fri, 16 Oct 2020 05:49:00: end of X-cor INFO @ Fri, 16 Oct 2020 05:49:00: #2 finished! INFO @ Fri, 16 Oct 2020 05:49:00: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 05:49:00: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 16 Oct 2020 05:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.05_model.r INFO @ Fri, 16 Oct 2020 05:49:00: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:49:01: 26000000 INFO @ Fri, 16 Oct 2020 05:49:06: 31000000 INFO @ Fri, 16 Oct 2020 05:49:08: 27000000 INFO @ Fri, 16 Oct 2020 05:49:13: 32000000 INFO @ Fri, 16 Oct 2020 05:49:15: 28000000 INFO @ Fri, 16 Oct 2020 05:49:19: 33000000 INFO @ Fri, 16 Oct 2020 05:49:21: 29000000 INFO @ Fri, 16 Oct 2020 05:49:26: 34000000 INFO @ Fri, 16 Oct 2020 05:49:28: 30000000 INFO @ Fri, 16 Oct 2020 05:49:33: 35000000 INFO @ Fri, 16 Oct 2020 05:49:35: 31000000 INFO @ Fri, 16 Oct 2020 05:49:39: 36000000 INFO @ Fri, 16 Oct 2020 05:49:42: 32000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 05:49:47: 37000000 INFO @ Fri, 16 Oct 2020 05:49:49: 33000000 INFO @ Fri, 16 Oct 2020 05:49:53: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:49:53: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:49:53: #1 total tags in treatment: 37912187 INFO @ Fri, 16 Oct 2020 05:49:53: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:49:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:49:54: #1 tags after filtering in treatment: 37912066 INFO @ Fri, 16 Oct 2020 05:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:49:54: #1 finished! INFO @ Fri, 16 Oct 2020 05:49:54: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:49:55: 34000000 INFO @ Fri, 16 Oct 2020 05:49:58: #2 number of paired peaks: 34889 INFO @ Fri, 16 Oct 2020 05:49:58: start model_add_line... INFO @ Fri, 16 Oct 2020 05:49:59: start X-correlation... INFO @ Fri, 16 Oct 2020 05:49:59: end of X-cor INFO @ Fri, 16 Oct 2020 05:49:59: #2 finished! INFO @ Fri, 16 Oct 2020 05:49:59: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 05:49:59: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 16 Oct 2020 05:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.10_model.r INFO @ Fri, 16 Oct 2020 05:49:59: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:50:02: 35000000 INFO @ Fri, 16 Oct 2020 05:50:08: 36000000 INFO @ Fri, 16 Oct 2020 05:50:15: 37000000 INFO @ Fri, 16 Oct 2020 05:50:21: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:50:21: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:50:21: #1 total tags in treatment: 37912187 INFO @ Fri, 16 Oct 2020 05:50:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:50:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 05:50:22: #1 tags after filtering in treatment: 37912066 INFO @ Fri, 16 Oct 2020 05:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:50:22: #1 finished! INFO @ Fri, 16 Oct 2020 05:50:22: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:50:26: #2 number of paired peaks: 34889 INFO @ Fri, 16 Oct 2020 05:50:26: start model_add_line... INFO @ Fri, 16 Oct 2020 05:50:27: start X-correlation... INFO @ Fri, 16 Oct 2020 05:50:27: end of X-cor INFO @ Fri, 16 Oct 2020 05:50:27: #2 finished! INFO @ Fri, 16 Oct 2020 05:50:27: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 05:50:27: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 16 Oct 2020 05:50:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.20_model.r INFO @ Fri, 16 Oct 2020 05:50:27: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:50:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:50:30: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.05_peaks.xls INFO @ Fri, 16 Oct 2020 05:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.05_summits.bed INFO @ Fri, 16 Oct 2020 05:51:15: Done! pass1 - making usageList (142 chroms): 28 millis pass2 - checking and writing primary data (24860 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:51:29: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:51:59: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:52:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.10_peaks.xls INFO @ Fri, 16 Oct 2020 05:52:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:52:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.10_summits.bed INFO @ Fri, 16 Oct 2020 05:52:14: Done! pass1 - making usageList (133 chroms): 5 millis pass2 - checking and writing primary data (22342 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:52:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.20_peaks.xls INFO @ Fri, 16 Oct 2020 05:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745121/ERX2745121.20_summits.bed INFO @ Fri, 16 Oct 2020 05:52:44: Done! pass1 - making usageList (118 chroms): 3 millis pass2 - checking and writing primary data (19494 records, 4 fields): 38 millis CompletedMACS2peakCalling