Job ID = 10223639 SRX = ERX2745120 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T19:42:33 prefetch.2.10.7: 1) Downloading 'ERR2731895'... 2020-10-15T19:42:33 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T19:44:42 prefetch.2.10.7: HTTPS download succeed 2020-10-15T19:44:42 prefetch.2.10.7: 1) 'ERR2731895' was downloaded successfully Read 93292788 spots for ERR2731895/ERR2731895.sra Written 93292788 spots for ERR2731895/ERR2731895.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: 00:00:03 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:44:28 93292788 reads; of these: 93292788 (100.00%) were unpaired; of these: 3057713 (3.28%) aligned 0 times 75141597 (80.54%) aligned exactly 1 time 15093478 (16.18%) aligned >1 times 96.72% overall alignment rate Time searching: 00:44:36 Overall time: 00:44:36 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 40 files... [bam_rmdupse_core] 45310253 / 90235075 = 0.5021 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 05:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.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 05:45:23: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:45:23: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:45:28: 1000000 INFO @ Fri, 16 Oct 2020 05:45:32: 2000000 INFO @ Fri, 16 Oct 2020 05:45:36: 3000000 INFO @ Fri, 16 Oct 2020 05:45:41: 4000000 INFO @ Fri, 16 Oct 2020 05:45:45: 5000000 INFO @ Fri, 16 Oct 2020 05:45:50: 6000000 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 05:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.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 05:45:53: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:45:53: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:45:54: 7000000 INFO @ Fri, 16 Oct 2020 05:45:58: 1000000 INFO @ Fri, 16 Oct 2020 05:45:58: 8000000 INFO @ Fri, 16 Oct 2020 05:46:02: 2000000 INFO @ Fri, 16 Oct 2020 05:46:03: 9000000 INFO @ Fri, 16 Oct 2020 05:46:07: 3000000 INFO @ Fri, 16 Oct 2020 05:46:08: 10000000 INFO @ Fri, 16 Oct 2020 05:46:11: 4000000 INFO @ Fri, 16 Oct 2020 05:46:12: 11000000 INFO @ Fri, 16 Oct 2020 05:46:16: 5000000 INFO @ Fri, 16 Oct 2020 05:46:17: 12000000 INFO @ Fri, 16 Oct 2020 05:46:20: 6000000 INFO @ Fri, 16 Oct 2020 05:46:21: 13000000 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 05:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.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 05:46:23: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:46:23: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:46:25: 7000000 INFO @ Fri, 16 Oct 2020 05:46:26: 14000000 INFO @ Fri, 16 Oct 2020 05:46:28: 1000000 INFO @ Fri, 16 Oct 2020 05:46:29: 8000000 INFO @ Fri, 16 Oct 2020 05:46:30: 15000000 INFO @ Fri, 16 Oct 2020 05:46:32: 2000000 INFO @ Fri, 16 Oct 2020 05:46:34: 9000000 INFO @ Fri, 16 Oct 2020 05:46:35: 16000000 INFO @ Fri, 16 Oct 2020 05:46:37: 3000000 INFO @ Fri, 16 Oct 2020 05:46:39: 10000000 INFO @ Fri, 16 Oct 2020 05:46:39: 17000000 INFO @ Fri, 16 Oct 2020 05:46:41: 4000000 INFO @ Fri, 16 Oct 2020 05:46:43: 11000000 INFO @ Fri, 16 Oct 2020 05:46:44: 18000000 INFO @ Fri, 16 Oct 2020 05:46:46: 5000000 INFO @ Fri, 16 Oct 2020 05:46:48: 12000000 INFO @ Fri, 16 Oct 2020 05:46:49: 19000000 INFO @ Fri, 16 Oct 2020 05:46:51: 6000000 INFO @ Fri, 16 Oct 2020 05:46:52: 13000000 INFO @ Fri, 16 Oct 2020 05:46:53: 20000000 INFO @ Fri, 16 Oct 2020 05:46:55: 7000000 INFO @ Fri, 16 Oct 2020 05:46:57: 14000000 INFO @ Fri, 16 Oct 2020 05:46:58: 21000000 INFO @ Fri, 16 Oct 2020 05:47:00: 8000000 INFO @ Fri, 16 Oct 2020 05:47:01: 15000000 INFO @ Fri, 16 Oct 2020 05:47:02: 22000000 INFO @ Fri, 16 Oct 2020 05:47:04: 9000000 INFO @ Fri, 16 Oct 2020 05:47:06: 16000000 INFO @ Fri, 16 Oct 2020 05:47:07: 23000000 INFO @ Fri, 16 Oct 2020 05:47:09: 10000000 INFO @ Fri, 16 Oct 2020 05:47:11: 17000000 INFO @ Fri, 16 Oct 2020 05:47:11: 24000000 INFO @ Fri, 16 Oct 2020 05:47:13: 11000000 INFO @ Fri, 16 Oct 2020 05:47:15: 18000000 INFO @ Fri, 16 Oct 2020 05:47:16: 25000000 INFO @ Fri, 16 Oct 2020 05:47:18: 12000000 INFO @ Fri, 16 Oct 2020 05:47:20: 19000000 INFO @ Fri, 16 Oct 2020 05:47:21: 26000000 INFO @ Fri, 16 Oct 2020 05:47:22: 13000000 INFO @ Fri, 16 Oct 2020 05:47:24: 20000000 INFO @ Fri, 16 Oct 2020 05:47:25: 27000000 INFO @ Fri, 16 Oct 2020 05:47:27: 14000000 INFO @ Fri, 16 Oct 2020 05:47:29: 21000000 INFO @ Fri, 16 Oct 2020 05:47:30: 28000000 INFO @ Fri, 16 Oct 2020 05:47:31: 15000000 INFO @ Fri, 16 Oct 2020 05:47:33: 22000000 INFO @ Fri, 16 Oct 2020 05:47:34: 29000000 INFO @ Fri, 16 Oct 2020 05:47:36: 16000000 INFO @ Fri, 16 Oct 2020 05:47:38: 23000000 INFO @ Fri, 16 Oct 2020 05:47:39: 30000000 INFO @ Fri, 16 Oct 2020 05:47:41: 17000000 INFO @ Fri, 16 Oct 2020 05:47:43: 24000000 INFO @ Fri, 16 Oct 2020 05:47:43: 31000000 INFO @ Fri, 16 Oct 2020 05:47:45: 18000000 INFO @ Fri, 16 Oct 2020 05:47:47: 25000000 INFO @ Fri, 16 Oct 2020 05:47:48: 32000000 INFO @ Fri, 16 Oct 2020 05:47:50: 19000000 INFO @ Fri, 16 Oct 2020 05:47:52: 26000000 INFO @ Fri, 16 Oct 2020 05:47:52: 33000000 INFO @ Fri, 16 Oct 2020 05:47:54: 20000000 INFO @ Fri, 16 Oct 2020 05:47:56: 27000000 INFO @ Fri, 16 Oct 2020 05:47:57: 34000000 INFO @ Fri, 16 Oct 2020 05:47:59: 21000000 INFO @ Fri, 16 Oct 2020 05:48:01: 28000000 INFO @ Fri, 16 Oct 2020 05:48:02: 35000000 INFO @ Fri, 16 Oct 2020 05:48:03: 22000000 INFO @ Fri, 16 Oct 2020 05:48:05: 29000000 INFO @ Fri, 16 Oct 2020 05:48:06: 36000000 INFO @ Fri, 16 Oct 2020 05:48:08: 23000000 INFO @ Fri, 16 Oct 2020 05:48:10: 30000000 INFO @ Fri, 16 Oct 2020 05:48:11: 37000000 INFO @ Fri, 16 Oct 2020 05:48:13: 24000000 INFO @ Fri, 16 Oct 2020 05:48:14: 31000000 INFO @ Fri, 16 Oct 2020 05:48:15: 38000000 INFO @ Fri, 16 Oct 2020 05:48:17: 25000000 INFO @ Fri, 16 Oct 2020 05:48:19: 32000000 INFO @ Fri, 16 Oct 2020 05:48:20: 39000000 INFO @ Fri, 16 Oct 2020 05:48:22: 26000000 INFO @ Fri, 16 Oct 2020 05:48:24: 33000000 INFO @ Fri, 16 Oct 2020 05:48:25: 40000000 INFO @ Fri, 16 Oct 2020 05:48:26: 27000000 INFO @ Fri, 16 Oct 2020 05:48:28: 34000000 INFO @ Fri, 16 Oct 2020 05:48:29: 41000000 INFO @ Fri, 16 Oct 2020 05:48:31: 28000000 INFO @ Fri, 16 Oct 2020 05:48:33: 35000000 INFO @ Fri, 16 Oct 2020 05:48:34: 42000000 INFO @ Fri, 16 Oct 2020 05:48:35: 29000000 INFO @ Fri, 16 Oct 2020 05:48:37: 36000000 INFO @ Fri, 16 Oct 2020 05:48:38: 43000000 INFO @ Fri, 16 Oct 2020 05:48:40: 30000000 INFO @ Fri, 16 Oct 2020 05:48:42: 37000000 INFO @ Fri, 16 Oct 2020 05:48:43: 44000000 INFO @ Fri, 16 Oct 2020 05:48:44: 31000000 INFO @ Fri, 16 Oct 2020 05:48:46: 38000000 INFO @ Fri, 16 Oct 2020 05:48:48: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:48:48: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:48:48: #1 total tags in treatment: 44924822 INFO @ Fri, 16 Oct 2020 05:48:48: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:48:48: #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 05:48:48: #1 tags after filtering in treatment: 44924618 INFO @ Fri, 16 Oct 2020 05:48:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:48:48: #1 finished! INFO @ Fri, 16 Oct 2020 05:48:48: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:48:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:48:49: 32000000 INFO @ Fri, 16 Oct 2020 05:48:51: 39000000 INFO @ Fri, 16 Oct 2020 05:48:53: 33000000 INFO @ Fri, 16 Oct 2020 05:48:56: 40000000 INFO @ Fri, 16 Oct 2020 05:48:57: #2 number of paired peaks: 116376 INFO @ Fri, 16 Oct 2020 05:48:57: start model_add_line... INFO @ Fri, 16 Oct 2020 05:48:58: start X-correlation... INFO @ Fri, 16 Oct 2020 05:48:58: end of X-cor INFO @ Fri, 16 Oct 2020 05:48:58: #2 finished! INFO @ Fri, 16 Oct 2020 05:48:58: #2 predicted fragment length is 242 bps INFO @ Fri, 16 Oct 2020 05:48:58: #2 alternative fragment length(s) may be 242 bps INFO @ Fri, 16 Oct 2020 05:48:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.05_model.r INFO @ Fri, 16 Oct 2020 05:48:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:48:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:48:58: 34000000 INFO @ Fri, 16 Oct 2020 05:49:01: 41000000 INFO @ Fri, 16 Oct 2020 05:49:02: 35000000 INFO @ Fri, 16 Oct 2020 05:49:06: 42000000 INFO @ Fri, 16 Oct 2020 05:49:07: 36000000 INFO @ Fri, 16 Oct 2020 05:49:10: 43000000 INFO @ Fri, 16 Oct 2020 05:49:12: 37000000 INFO @ Fri, 16 Oct 2020 05:49:15: 44000000 INFO @ Fri, 16 Oct 2020 05:49:16: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 05:49:20: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:49:20: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:49:20: #1 total tags in treatment: 44924822 INFO @ Fri, 16 Oct 2020 05:49:20: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:49:20: #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 05:49:20: #1 tags after filtering in treatment: 44924618 INFO @ Fri, 16 Oct 2020 05:49:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:49:20: #1 finished! INFO @ Fri, 16 Oct 2020 05:49:20: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:49:21: 39000000 INFO @ Fri, 16 Oct 2020 05:49:25: 40000000 INFO @ Fri, 16 Oct 2020 05:49:29: #2 number of paired peaks: 116376 INFO @ Fri, 16 Oct 2020 05:49:29: start model_add_line... INFO @ Fri, 16 Oct 2020 05:49:30: start X-correlation... INFO @ Fri, 16 Oct 2020 05:49:30: end of X-cor INFO @ Fri, 16 Oct 2020 05:49:30: #2 finished! INFO @ Fri, 16 Oct 2020 05:49:30: #2 predicted fragment length is 242 bps INFO @ Fri, 16 Oct 2020 05:49:30: #2 alternative fragment length(s) may be 242 bps INFO @ Fri, 16 Oct 2020 05:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.10_model.r INFO @ Fri, 16 Oct 2020 05:49:30: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:49:30: 41000000 INFO @ Fri, 16 Oct 2020 05:49:34: 42000000 INFO @ Fri, 16 Oct 2020 05:49:39: 43000000 INFO @ Fri, 16 Oct 2020 05:49:43: 44000000 INFO @ Fri, 16 Oct 2020 05:49:48: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:49:48: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:49:48: #1 total tags in treatment: 44924822 INFO @ Fri, 16 Oct 2020 05:49:48: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:49:48: #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 05:49:49: #1 tags after filtering in treatment: 44924618 INFO @ Fri, 16 Oct 2020 05:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:49:49: #1 finished! INFO @ Fri, 16 Oct 2020 05:49:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:49:57: #2 number of paired peaks: 116376 INFO @ Fri, 16 Oct 2020 05:49:57: start model_add_line... INFO @ Fri, 16 Oct 2020 05:49:58: start X-correlation... INFO @ Fri, 16 Oct 2020 05:49:58: end of X-cor INFO @ Fri, 16 Oct 2020 05:49:58: #2 finished! INFO @ Fri, 16 Oct 2020 05:49:58: #2 predicted fragment length is 242 bps INFO @ Fri, 16 Oct 2020 05:49:58: #2 alternative fragment length(s) may be 242 bps INFO @ Fri, 16 Oct 2020 05:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.20_model.r INFO @ Fri, 16 Oct 2020 05:49:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:49:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 05:50:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:51:22: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:51:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.05_peaks.xls INFO @ Fri, 16 Oct 2020 05:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.05_summits.bed INFO @ Fri, 16 Oct 2020 05:51:50: Done! pass1 - making usageList (233 chroms): 8 millis pass2 - checking and writing primary data (61515 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:51:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.10_peaks.xls INFO @ Fri, 16 Oct 2020 05:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.10_summits.bed INFO @ Fri, 16 Oct 2020 05:52:21: Done! pass1 - making usageList (204 chroms): 7 millis pass2 - checking and writing primary data (50291 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.20_peaks.xls INFO @ Fri, 16 Oct 2020 05:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745120/ERX2745120.20_summits.bed INFO @ Fri, 16 Oct 2020 05:52:50: Done! pass1 - making usageList (177 chroms): 5 millis pass2 - checking and writing primary data (37138 records, 4 fields): 39 millis CompletedMACS2peakCalling