Job ID = 10223606 SRX = ERX2745105 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T18:43:48 prefetch.2.10.7: 1) Downloading 'ERR2731880'... 2020-10-15T18:43:48 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T18:45:08 prefetch.2.10.7: HTTPS download succeed 2020-10-15T18:45:08 prefetch.2.10.7: 1) 'ERR2731880' was downloaded successfully Read 56028721 spots for ERR2731880/ERR2731880.sra Written 56028721 spots for ERR2731880/ERR2731880.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: 00:33:36 56028721 reads; of these: 56028721 (100.00%) were unpaired; of these: 1777307 (3.17%) aligned 0 times 47976758 (85.63%) aligned exactly 1 time 6274656 (11.20%) aligned >1 times 96.83% overall alignment rate Time searching: 00:33:41 Overall time: 00:33:41 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] 11499324 / 54251414 = 0.2120 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 04:30:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.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 04:30:29: #1 read tag files... INFO @ Fri, 16 Oct 2020 04:30:29: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 04:30:34: 1000000 INFO @ Fri, 16 Oct 2020 04:30:39: 2000000 INFO @ Fri, 16 Oct 2020 04:30:45: 3000000 INFO @ Fri, 16 Oct 2020 04:30:50: 4000000 INFO @ Fri, 16 Oct 2020 04:30:55: 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 04:30:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.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 04:30:58: #1 read tag files... INFO @ Fri, 16 Oct 2020 04:30:58: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 04:31:01: 6000000 INFO @ Fri, 16 Oct 2020 04:31:05: 1000000 INFO @ Fri, 16 Oct 2020 04:31:07: 7000000 INFO @ Fri, 16 Oct 2020 04:31:11: 2000000 INFO @ Fri, 16 Oct 2020 04:31:13: 8000000 INFO @ Fri, 16 Oct 2020 04:31:17: 3000000 INFO @ Fri, 16 Oct 2020 04:31:19: 9000000 INFO @ Fri, 16 Oct 2020 04:31:23: 4000000 INFO @ Fri, 16 Oct 2020 04:31:25: 10000000 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 04:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.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 04:31:28: #1 read tag files... INFO @ Fri, 16 Oct 2020 04:31:28: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 04:31:29: 5000000 INFO @ Fri, 16 Oct 2020 04:31:31: 11000000 INFO @ Fri, 16 Oct 2020 04:31:35: 1000000 INFO @ Fri, 16 Oct 2020 04:31:35: 6000000 INFO @ Fri, 16 Oct 2020 04:31:38: 12000000 INFO @ Fri, 16 Oct 2020 04:31:41: 2000000 INFO @ Fri, 16 Oct 2020 04:31:41: 7000000 INFO @ Fri, 16 Oct 2020 04:31:44: 13000000 INFO @ Fri, 16 Oct 2020 04:31:47: 3000000 INFO @ Fri, 16 Oct 2020 04:31:48: 8000000 INFO @ Fri, 16 Oct 2020 04:31:50: 14000000 INFO @ Fri, 16 Oct 2020 04:31:53: 4000000 INFO @ Fri, 16 Oct 2020 04:31:54: 9000000 INFO @ Fri, 16 Oct 2020 04:31:56: 15000000 INFO @ Fri, 16 Oct 2020 04:31:59: 5000000 INFO @ Fri, 16 Oct 2020 04:32:00: 10000000 INFO @ Fri, 16 Oct 2020 04:32:02: 16000000 INFO @ Fri, 16 Oct 2020 04:32:05: 6000000 INFO @ Fri, 16 Oct 2020 04:32:06: 11000000 INFO @ Fri, 16 Oct 2020 04:32:09: 17000000 INFO @ Fri, 16 Oct 2020 04:32:11: 7000000 INFO @ Fri, 16 Oct 2020 04:32:12: 12000000 INFO @ Fri, 16 Oct 2020 04:32:15: 18000000 INFO @ Fri, 16 Oct 2020 04:32:17: 8000000 INFO @ Fri, 16 Oct 2020 04:32:19: 13000000 INFO @ Fri, 16 Oct 2020 04:32:21: 19000000 INFO @ Fri, 16 Oct 2020 04:32:23: 9000000 INFO @ Fri, 16 Oct 2020 04:32:25: 14000000 INFO @ Fri, 16 Oct 2020 04:32:27: 20000000 INFO @ Fri, 16 Oct 2020 04:32:30: 10000000 INFO @ Fri, 16 Oct 2020 04:32:31: 15000000 INFO @ Fri, 16 Oct 2020 04:32:33: 21000000 INFO @ Fri, 16 Oct 2020 04:32:36: 11000000 INFO @ Fri, 16 Oct 2020 04:32:37: 16000000 INFO @ Fri, 16 Oct 2020 04:32:40: 22000000 INFO @ Fri, 16 Oct 2020 04:32:42: 12000000 INFO @ Fri, 16 Oct 2020 04:32:43: 17000000 INFO @ Fri, 16 Oct 2020 04:32:46: 23000000 INFO @ Fri, 16 Oct 2020 04:32:48: 13000000 INFO @ Fri, 16 Oct 2020 04:32:50: 18000000 INFO @ Fri, 16 Oct 2020 04:32:52: 24000000 INFO @ Fri, 16 Oct 2020 04:32:54: 14000000 INFO @ Fri, 16 Oct 2020 04:32:56: 19000000 INFO @ Fri, 16 Oct 2020 04:32:58: 25000000 INFO @ Fri, 16 Oct 2020 04:33:00: 15000000 INFO @ Fri, 16 Oct 2020 04:33:02: 20000000 INFO @ Fri, 16 Oct 2020 04:33:04: 26000000 INFO @ Fri, 16 Oct 2020 04:33:06: 16000000 INFO @ Fri, 16 Oct 2020 04:33:08: 21000000 INFO @ Fri, 16 Oct 2020 04:33:10: 27000000 INFO @ Fri, 16 Oct 2020 04:33:12: 17000000 INFO @ Fri, 16 Oct 2020 04:33:14: 22000000 INFO @ Fri, 16 Oct 2020 04:33:16: 28000000 INFO @ Fri, 16 Oct 2020 04:33:18: 18000000 INFO @ Fri, 16 Oct 2020 04:33:21: 23000000 INFO @ Fri, 16 Oct 2020 04:33:23: 29000000 INFO @ Fri, 16 Oct 2020 04:33:24: 19000000 INFO @ Fri, 16 Oct 2020 04:33:27: 24000000 INFO @ Fri, 16 Oct 2020 04:33:29: 30000000 INFO @ Fri, 16 Oct 2020 04:33:30: 20000000 INFO @ Fri, 16 Oct 2020 04:33:33: 25000000 INFO @ Fri, 16 Oct 2020 04:33:35: 31000000 INFO @ Fri, 16 Oct 2020 04:33:37: 21000000 INFO @ Fri, 16 Oct 2020 04:33:39: 26000000 INFO @ Fri, 16 Oct 2020 04:33:41: 32000000 INFO @ Fri, 16 Oct 2020 04:33:43: 22000000 INFO @ Fri, 16 Oct 2020 04:33:45: 27000000 INFO @ Fri, 16 Oct 2020 04:33:48: 33000000 INFO @ Fri, 16 Oct 2020 04:33:49: 23000000 INFO @ Fri, 16 Oct 2020 04:33:51: 28000000 INFO @ Fri, 16 Oct 2020 04:33:54: 34000000 INFO @ Fri, 16 Oct 2020 04:33:55: 24000000 INFO @ Fri, 16 Oct 2020 04:33:58: 29000000 INFO @ Fri, 16 Oct 2020 04:34:00: 35000000 INFO @ Fri, 16 Oct 2020 04:34:01: 25000000 INFO @ Fri, 16 Oct 2020 04:34:04: 30000000 INFO @ Fri, 16 Oct 2020 04:34:06: 36000000 INFO @ Fri, 16 Oct 2020 04:34:07: 26000000 INFO @ Fri, 16 Oct 2020 04:34:10: 31000000 INFO @ Fri, 16 Oct 2020 04:34:12: 37000000 INFO @ Fri, 16 Oct 2020 04:34:13: 27000000 INFO @ Fri, 16 Oct 2020 04:34:16: 32000000 INFO @ Fri, 16 Oct 2020 04:34:18: 38000000 INFO @ Fri, 16 Oct 2020 04:34:19: 28000000 INFO @ Fri, 16 Oct 2020 04:34:22: 33000000 INFO @ Fri, 16 Oct 2020 04:34:25: 39000000 INFO @ Fri, 16 Oct 2020 04:34:25: 29000000 INFO @ Fri, 16 Oct 2020 04:34:29: 34000000 INFO @ Fri, 16 Oct 2020 04:34:31: 40000000 INFO @ Fri, 16 Oct 2020 04:34:31: 30000000 INFO @ Fri, 16 Oct 2020 04:34:35: 35000000 INFO @ Fri, 16 Oct 2020 04:34:37: 41000000 INFO @ Fri, 16 Oct 2020 04:34:38: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 04:34:41: 36000000 INFO @ Fri, 16 Oct 2020 04:34:43: 42000000 INFO @ Fri, 16 Oct 2020 04:34:44: 32000000 INFO @ Fri, 16 Oct 2020 04:34:47: 37000000 INFO @ Fri, 16 Oct 2020 04:34:48: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 04:34:48: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 04:34:48: #1 total tags in treatment: 42752090 INFO @ Fri, 16 Oct 2020 04:34:48: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 04:34:48: #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 04:34:49: #1 tags after filtering in treatment: 42751922 INFO @ Fri, 16 Oct 2020 04:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 04:34:49: #1 finished! INFO @ Fri, 16 Oct 2020 04:34:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 04:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 04:34:50: 33000000 INFO @ Fri, 16 Oct 2020 04:34:53: 38000000 INFO @ Fri, 16 Oct 2020 04:34:56: 34000000 INFO @ Fri, 16 Oct 2020 04:34:56: #2 number of paired peaks: 114619 INFO @ Fri, 16 Oct 2020 04:34:56: start model_add_line... INFO @ Fri, 16 Oct 2020 04:34:57: start X-correlation... INFO @ Fri, 16 Oct 2020 04:34:57: end of X-cor INFO @ Fri, 16 Oct 2020 04:34:57: #2 finished! INFO @ Fri, 16 Oct 2020 04:34:57: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Oct 2020 04:34:57: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Oct 2020 04:34:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.05_model.r INFO @ Fri, 16 Oct 2020 04:34:57: #3 Call peaks... INFO @ Fri, 16 Oct 2020 04:34:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 04:34:59: 39000000 INFO @ Fri, 16 Oct 2020 04:35:02: 35000000 INFO @ Fri, 16 Oct 2020 04:35:05: 40000000 INFO @ Fri, 16 Oct 2020 04:35:08: 36000000 INFO @ Fri, 16 Oct 2020 04:35:12: 41000000 INFO @ Fri, 16 Oct 2020 04:35:14: 37000000 INFO @ Fri, 16 Oct 2020 04:35:18: 42000000 INFO @ Fri, 16 Oct 2020 04:35:20: 38000000 INFO @ Fri, 16 Oct 2020 04:35:23: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 04:35:23: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 04:35:23: #1 total tags in treatment: 42752090 INFO @ Fri, 16 Oct 2020 04:35:23: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 04:35:23: #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 04:35:24: #1 tags after filtering in treatment: 42751922 INFO @ Fri, 16 Oct 2020 04:35:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 04:35:24: #1 finished! INFO @ Fri, 16 Oct 2020 04:35:24: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 04:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 04:35:26: 39000000 INFO @ Fri, 16 Oct 2020 04:35:31: #2 number of paired peaks: 114619 INFO @ Fri, 16 Oct 2020 04:35:31: start model_add_line... INFO @ Fri, 16 Oct 2020 04:35:31: start X-correlation... INFO @ Fri, 16 Oct 2020 04:35:31: end of X-cor INFO @ Fri, 16 Oct 2020 04:35:31: #2 finished! INFO @ Fri, 16 Oct 2020 04:35:31: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Oct 2020 04:35:31: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Oct 2020 04:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.10_model.r INFO @ Fri, 16 Oct 2020 04:35:31: #3 Call peaks... INFO @ Fri, 16 Oct 2020 04:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 04:35:32: 40000000 INFO @ Fri, 16 Oct 2020 04:35:38: 41000000 INFO @ Fri, 16 Oct 2020 04:35:44: 42000000 INFO @ Fri, 16 Oct 2020 04:35:48: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 04:35:48: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 04:35:48: #1 total tags in treatment: 42752090 INFO @ Fri, 16 Oct 2020 04:35:48: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 04:35:48: #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 04:35:49: #1 tags after filtering in treatment: 42751922 INFO @ Fri, 16 Oct 2020 04:35:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 04:35:49: #1 finished! INFO @ Fri, 16 Oct 2020 04:35:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 04:35:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 04:35:56: #2 number of paired peaks: 114619 INFO @ Fri, 16 Oct 2020 04:35:56: start model_add_line... INFO @ Fri, 16 Oct 2020 04:35:56: start X-correlation... INFO @ Fri, 16 Oct 2020 04:35:56: end of X-cor INFO @ Fri, 16 Oct 2020 04:35:56: #2 finished! INFO @ Fri, 16 Oct 2020 04:35:56: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Oct 2020 04:35:56: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 16 Oct 2020 04:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.20_model.r INFO @ Fri, 16 Oct 2020 04:35:56: #3 Call peaks... INFO @ Fri, 16 Oct 2020 04:35:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 04:36:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 04:37:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 04:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.05_peaks.xls INFO @ Fri, 16 Oct 2020 04:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 04:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.05_summits.bed INFO @ Fri, 16 Oct 2020 04:37:40: Done! INFO @ Fri, 16 Oct 2020 04:37:41: #3 Call peaks for each chromosome... pass1 - making usageList (137 chroms): 5 millis pass2 - checking and writing primary data (38892 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 04:38:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.10_peaks.xls INFO @ Fri, 16 Oct 2020 04:38:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 04:38:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.10_summits.bed INFO @ Fri, 16 Oct 2020 04:38:16: Done! pass1 - making usageList (107 chroms): 4 millis pass2 - checking and writing primary data (24016 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 04:38:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.20_peaks.xls INFO @ Fri, 16 Oct 2020 04:38:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 04:38:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745105/ERX2745105.20_summits.bed INFO @ Fri, 16 Oct 2020 04:38:38: Done! pass1 - making usageList (75 chroms): 3 millis pass2 - checking and writing primary data (14430 records, 4 fields): 15 millis CompletedMACS2peakCalling