Job ID = 10223649 SRX = ERX2745125 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T19:52:47 prefetch.2.10.7: 1) Downloading 'ERR2731900'... 2020-10-15T19:52:47 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T19:54:34 prefetch.2.10.7: HTTPS download succeed 2020-10-15T19:54:34 prefetch.2.10.7: 1) 'ERR2731900' was downloaded successfully Read 74934449 spots for ERR2731900/ERR2731900.sra Written 74934449 spots for ERR2731900/ERR2731900.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: 00:31:48 74934449 reads; of these: 74934449 (100.00%) were unpaired; of these: 3556751 (4.75%) aligned 0 times 62487566 (83.39%) aligned exactly 1 time 8890132 (11.86%) aligned >1 times 95.25% overall alignment rate Time searching: 00:31:50 Overall time: 00:31:50 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 32 files... [bam_rmdupse_core] 42167223 / 71377698 = 0.5908 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 05:39:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.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 05:39:00: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:39:00: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:39:05: 1000000 INFO @ Fri, 16 Oct 2020 05:39:10: 2000000 INFO @ Fri, 16 Oct 2020 05:39:14: 3000000 INFO @ Fri, 16 Oct 2020 05:39:18: 4000000 INFO @ Fri, 16 Oct 2020 05:39:23: 5000000 INFO @ Fri, 16 Oct 2020 05:39:27: 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 05:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.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 05:39:30: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:39:30: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:39:32: 7000000 INFO @ Fri, 16 Oct 2020 05:39:35: 1000000 INFO @ Fri, 16 Oct 2020 05:39:37: 8000000 INFO @ Fri, 16 Oct 2020 05:39:39: 2000000 INFO @ Fri, 16 Oct 2020 05:39:41: 9000000 INFO @ Fri, 16 Oct 2020 05:39:44: 3000000 INFO @ Fri, 16 Oct 2020 05:39:46: 10000000 INFO @ Fri, 16 Oct 2020 05:39:49: 4000000 INFO @ Fri, 16 Oct 2020 05:39:51: 11000000 INFO @ Fri, 16 Oct 2020 05:39:53: 5000000 INFO @ Fri, 16 Oct 2020 05:39:55: 12000000 INFO @ Fri, 16 Oct 2020 05:39:58: 6000000 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 05:40:00: 13000000 INFO @ Fri, 16 Oct 2020 05:40:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.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 05:40:00: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:40:00: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:40:03: 7000000 INFO @ Fri, 16 Oct 2020 05:40:04: 14000000 INFO @ Fri, 16 Oct 2020 05:40:05: 1000000 INFO @ Fri, 16 Oct 2020 05:40:07: 8000000 INFO @ Fri, 16 Oct 2020 05:40:09: 15000000 INFO @ Fri, 16 Oct 2020 05:40:10: 2000000 INFO @ Fri, 16 Oct 2020 05:40:12: 9000000 INFO @ Fri, 16 Oct 2020 05:40:14: 16000000 INFO @ Fri, 16 Oct 2020 05:40:15: 3000000 INFO @ Fri, 16 Oct 2020 05:40:17: 10000000 INFO @ Fri, 16 Oct 2020 05:40:18: 17000000 INFO @ Fri, 16 Oct 2020 05:40:20: 4000000 INFO @ Fri, 16 Oct 2020 05:40:21: 11000000 INFO @ Fri, 16 Oct 2020 05:40:23: 18000000 INFO @ Fri, 16 Oct 2020 05:40:26: 5000000 INFO @ Fri, 16 Oct 2020 05:40:26: 12000000 INFO @ Fri, 16 Oct 2020 05:40:28: 19000000 INFO @ Fri, 16 Oct 2020 05:40:31: 13000000 INFO @ Fri, 16 Oct 2020 05:40:31: 6000000 INFO @ Fri, 16 Oct 2020 05:40:32: 20000000 INFO @ Fri, 16 Oct 2020 05:40:35: 14000000 INFO @ Fri, 16 Oct 2020 05:40:36: 7000000 INFO @ Fri, 16 Oct 2020 05:40:37: 21000000 INFO @ Fri, 16 Oct 2020 05:40:40: 15000000 INFO @ Fri, 16 Oct 2020 05:40:41: 8000000 INFO @ Fri, 16 Oct 2020 05:40:41: 22000000 INFO @ Fri, 16 Oct 2020 05:40:45: 16000000 INFO @ Fri, 16 Oct 2020 05:40:46: 23000000 INFO @ Fri, 16 Oct 2020 05:40:46: 9000000 INFO @ Fri, 16 Oct 2020 05:40:49: 17000000 INFO @ Fri, 16 Oct 2020 05:40:51: 24000000 INFO @ Fri, 16 Oct 2020 05:40:51: 10000000 INFO @ Fri, 16 Oct 2020 05:40:54: 18000000 INFO @ Fri, 16 Oct 2020 05:40:55: 25000000 INFO @ Fri, 16 Oct 2020 05:40:57: 11000000 INFO @ Fri, 16 Oct 2020 05:40:59: 19000000 INFO @ Fri, 16 Oct 2020 05:41:00: 26000000 INFO @ Fri, 16 Oct 2020 05:41:02: 12000000 INFO @ Fri, 16 Oct 2020 05:41:03: 20000000 INFO @ Fri, 16 Oct 2020 05:41:04: 27000000 INFO @ Fri, 16 Oct 2020 05:41:07: 13000000 INFO @ Fri, 16 Oct 2020 05:41:08: 21000000 INFO @ Fri, 16 Oct 2020 05:41:09: 28000000 INFO @ Fri, 16 Oct 2020 05:41:12: 14000000 INFO @ Fri, 16 Oct 2020 05:41:13: 22000000 INFO @ Fri, 16 Oct 2020 05:41:14: 29000000 INFO @ Fri, 16 Oct 2020 05:41:15: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:41:15: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:41:15: #1 total tags in treatment: 29210475 INFO @ Fri, 16 Oct 2020 05:41:15: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:41:15: #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 05:41:16: #1 tags after filtering in treatment: 29210305 INFO @ Fri, 16 Oct 2020 05:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:41:16: #1 finished! INFO @ Fri, 16 Oct 2020 05:41:16: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:41:17: 23000000 INFO @ Fri, 16 Oct 2020 05:41:17: 15000000 INFO @ Fri, 16 Oct 2020 05:41:19: #2 number of paired peaks: 35674 INFO @ Fri, 16 Oct 2020 05:41:19: start model_add_line... INFO @ Fri, 16 Oct 2020 05:41:20: start X-correlation... INFO @ Fri, 16 Oct 2020 05:41:20: end of X-cor INFO @ Fri, 16 Oct 2020 05:41:20: #2 finished! INFO @ Fri, 16 Oct 2020 05:41:20: #2 predicted fragment length is 234 bps INFO @ Fri, 16 Oct 2020 05:41:20: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 16 Oct 2020 05:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.05_model.r INFO @ Fri, 16 Oct 2020 05:41:20: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:41:22: 24000000 INFO @ Fri, 16 Oct 2020 05:41:23: 16000000 INFO @ Fri, 16 Oct 2020 05:41:26: 25000000 INFO @ Fri, 16 Oct 2020 05:41:28: 17000000 INFO @ Fri, 16 Oct 2020 05:41:31: 26000000 INFO @ Fri, 16 Oct 2020 05:41:33: 18000000 INFO @ Fri, 16 Oct 2020 05:41:36: 27000000 INFO @ Fri, 16 Oct 2020 05:41:38: 19000000 INFO @ Fri, 16 Oct 2020 05:41:40: 28000000 INFO @ Fri, 16 Oct 2020 05:41:43: 20000000 INFO @ Fri, 16 Oct 2020 05:41:45: 29000000 INFO @ Fri, 16 Oct 2020 05:41:46: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:41:46: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:41:46: #1 total tags in treatment: 29210475 INFO @ Fri, 16 Oct 2020 05:41:46: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:41:46: #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 05:41:47: #1 tags after filtering in treatment: 29210305 INFO @ Fri, 16 Oct 2020 05:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:41:47: #1 finished! INFO @ Fri, 16 Oct 2020 05:41:47: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:41:48: 21000000 INFO @ Fri, 16 Oct 2020 05:41:50: #2 number of paired peaks: 35674 INFO @ Fri, 16 Oct 2020 05:41:50: start model_add_line... INFO @ Fri, 16 Oct 2020 05:41:51: start X-correlation... INFO @ Fri, 16 Oct 2020 05:41:51: end of X-cor INFO @ Fri, 16 Oct 2020 05:41:51: #2 finished! INFO @ Fri, 16 Oct 2020 05:41:51: #2 predicted fragment length is 234 bps INFO @ Fri, 16 Oct 2020 05:41:51: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 16 Oct 2020 05:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.10_model.r INFO @ Fri, 16 Oct 2020 05:41:51: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:41:53: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 05:41:58: 23000000 INFO @ Fri, 16 Oct 2020 05:42:03: 24000000 INFO @ Fri, 16 Oct 2020 05:42:08: 25000000 INFO @ Fri, 16 Oct 2020 05:42:13: 26000000 INFO @ Fri, 16 Oct 2020 05:42:18: 27000000 INFO @ Fri, 16 Oct 2020 05:42:23: 28000000 INFO @ Fri, 16 Oct 2020 05:42:28: 29000000 INFO @ Fri, 16 Oct 2020 05:42:30: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:42:30: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:42:30: #1 total tags in treatment: 29210475 INFO @ Fri, 16 Oct 2020 05:42:30: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:42:30: #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 05:42:30: #1 tags after filtering in treatment: 29210305 INFO @ Fri, 16 Oct 2020 05:42:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:42:30: #1 finished! INFO @ Fri, 16 Oct 2020 05:42:30: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:42:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:42:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 05:42:34: #2 number of paired peaks: 35674 INFO @ Fri, 16 Oct 2020 05:42:34: start model_add_line... INFO @ Fri, 16 Oct 2020 05:42:34: start X-correlation... INFO @ Fri, 16 Oct 2020 05:42:34: end of X-cor INFO @ Fri, 16 Oct 2020 05:42:34: #2 finished! INFO @ Fri, 16 Oct 2020 05:42:34: #2 predicted fragment length is 234 bps INFO @ Fri, 16 Oct 2020 05:42:34: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 16 Oct 2020 05:42:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.20_model.r INFO @ Fri, 16 Oct 2020 05:42:34: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:43:05: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.05_peaks.xls INFO @ Fri, 16 Oct 2020 05:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.05_summits.bed INFO @ Fri, 16 Oct 2020 05:43:10: Done! pass1 - making usageList (137 chroms): 5 millis pass2 - checking and writing primary data (24913 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:43:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.10_peaks.xls INFO @ Fri, 16 Oct 2020 05:43:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:43:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.10_summits.bed INFO @ Fri, 16 Oct 2020 05:43:43: Done! pass1 - making usageList (124 chroms): 4 millis pass2 - checking and writing primary data (22202 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:43:48: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:44:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.20_peaks.xls INFO @ Fri, 16 Oct 2020 05:44:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:44:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745125/ERX2745125.20_summits.bed INFO @ Fri, 16 Oct 2020 05:44:27: Done! pass1 - making usageList (109 chroms): 3 millis pass2 - checking and writing primary data (19394 records, 4 fields): 21 millis CompletedMACS2peakCalling