Job ID = 6367710 SRX = SRX4012474 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:41:44 prefetch.2.10.7: 1) Downloading 'SRR7082715'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:56:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:56:00 prefetch.2.10.7: 1) 'SRR7082715' was downloaded successfully Read 36173858 spots for SRR7082715/SRR7082715.sra Written 36173858 spots for SRR7082715/SRR7082715.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:23:24 36173858 reads; of these: 36173858 (100.00%) were paired; of these: 26054897 (72.03%) aligned concordantly 0 times 2686559 (7.43%) aligned concordantly exactly 1 time 7432402 (20.55%) aligned concordantly >1 times ---- 26054897 pairs aligned concordantly 0 times; of these: 4088268 (15.69%) aligned discordantly 1 time ---- 21966629 pairs aligned 0 times concordantly or discordantly; of these: 43933258 mates make up the pairs; of these: 30253381 (68.86%) aligned 0 times 5151594 (11.73%) aligned exactly 1 time 8528283 (19.41%) aligned >1 times 58.18% overall alignment rate Time searching: 01:23:24 Overall time: 01:23:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 3433786 / 10889303 = 0.3153 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 @ Tue, 16 Jun 2020 10:40:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 10:40:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:40:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:40:39: 1000000 INFO @ Tue, 16 Jun 2020 10:40:45: 2000000 INFO @ Tue, 16 Jun 2020 10:40:51: 3000000 INFO @ Tue, 16 Jun 2020 10:40:57: 4000000 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 @ Tue, 16 Jun 2020 10:41:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 10:41:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:41:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:41:03: 5000000 INFO @ Tue, 16 Jun 2020 10:41:09: 1000000 INFO @ Tue, 16 Jun 2020 10:41:10: 6000000 INFO @ Tue, 16 Jun 2020 10:41:15: 2000000 INFO @ Tue, 16 Jun 2020 10:41:16: 7000000 INFO @ Tue, 16 Jun 2020 10:41:21: 3000000 INFO @ Tue, 16 Jun 2020 10:41:22: 8000000 INFO @ Tue, 16 Jun 2020 10:41:27: 4000000 INFO @ Tue, 16 Jun 2020 10:41:29: 9000000 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 @ Tue, 16 Jun 2020 10:41:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 10:41:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:41:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:41:34: 5000000 INFO @ Tue, 16 Jun 2020 10:41:35: 10000000 INFO @ Tue, 16 Jun 2020 10:41:40: 1000000 INFO @ Tue, 16 Jun 2020 10:41:40: 6000000 INFO @ Tue, 16 Jun 2020 10:41:41: 11000000 INFO @ Tue, 16 Jun 2020 10:41:46: 2000000 INFO @ Tue, 16 Jun 2020 10:41:46: 7000000 INFO @ Tue, 16 Jun 2020 10:41:48: 12000000 INFO @ Tue, 16 Jun 2020 10:41:52: 3000000 INFO @ Tue, 16 Jun 2020 10:41:52: 8000000 INFO @ Tue, 16 Jun 2020 10:41:54: 13000000 INFO @ Tue, 16 Jun 2020 10:41:58: 4000000 INFO @ Tue, 16 Jun 2020 10:41:59: 9000000 INFO @ Tue, 16 Jun 2020 10:42:00: 14000000 INFO @ Tue, 16 Jun 2020 10:42:05: 5000000 INFO @ Tue, 16 Jun 2020 10:42:05: 10000000 INFO @ Tue, 16 Jun 2020 10:42:07: 15000000 INFO @ Tue, 16 Jun 2020 10:42:11: 6000000 INFO @ Tue, 16 Jun 2020 10:42:11: 11000000 INFO @ Tue, 16 Jun 2020 10:42:13: 16000000 INFO @ Tue, 16 Jun 2020 10:42:18: 7000000 INFO @ Tue, 16 Jun 2020 10:42:18: 12000000 INFO @ Tue, 16 Jun 2020 10:42:20: 17000000 INFO @ Tue, 16 Jun 2020 10:42:24: 8000000 INFO @ Tue, 16 Jun 2020 10:42:24: 13000000 INFO @ Tue, 16 Jun 2020 10:42:26: 18000000 INFO @ Tue, 16 Jun 2020 10:42:30: 9000000 INFO @ Tue, 16 Jun 2020 10:42:30: 14000000 INFO @ Tue, 16 Jun 2020 10:42:33: 19000000 INFO @ Tue, 16 Jun 2020 10:42:37: 15000000 INFO @ Tue, 16 Jun 2020 10:42:37: 10000000 INFO @ Tue, 16 Jun 2020 10:42:39: 20000000 INFO @ Tue, 16 Jun 2020 10:42:43: 16000000 INFO @ Tue, 16 Jun 2020 10:42:43: 11000000 INFO @ Tue, 16 Jun 2020 10:42:45: 21000000 INFO @ Tue, 16 Jun 2020 10:42:49: 17000000 INFO @ Tue, 16 Jun 2020 10:42:49: 12000000 INFO @ Tue, 16 Jun 2020 10:42:51: 22000000 INFO @ Tue, 16 Jun 2020 10:42:55: 18000000 INFO @ Tue, 16 Jun 2020 10:42:55: 13000000 INFO @ Tue, 16 Jun 2020 10:42:57: 23000000 INFO @ Tue, 16 Jun 2020 10:43:01: 19000000 INFO @ Tue, 16 Jun 2020 10:43:01: 14000000 INFO @ Tue, 16 Jun 2020 10:43:03: 24000000 INFO @ Tue, 16 Jun 2020 10:43:07: 20000000 INFO @ Tue, 16 Jun 2020 10:43:08: 15000000 INFO @ Tue, 16 Jun 2020 10:43:09: 25000000 INFO @ Tue, 16 Jun 2020 10:43:13: 21000000 INFO @ Tue, 16 Jun 2020 10:43:14: 16000000 INFO @ Tue, 16 Jun 2020 10:43:15: 26000000 INFO @ Tue, 16 Jun 2020 10:43:19: 22000000 INFO @ Tue, 16 Jun 2020 10:43:20: 17000000 INFO @ Tue, 16 Jun 2020 10:43:21: 27000000 INFO @ Tue, 16 Jun 2020 10:43:25: 23000000 INFO @ Tue, 16 Jun 2020 10:43:26: 18000000 INFO @ Tue, 16 Jun 2020 10:43:27: 28000000 INFO @ Tue, 16 Jun 2020 10:43:31: 24000000 INFO @ Tue, 16 Jun 2020 10:43:32: 19000000 INFO @ Tue, 16 Jun 2020 10:43:33: 29000000 INFO @ Tue, 16 Jun 2020 10:43:37: 25000000 INFO @ Tue, 16 Jun 2020 10:43:39: 20000000 INFO @ Tue, 16 Jun 2020 10:43:40: 30000000 INFO @ Tue, 16 Jun 2020 10:43:43: 26000000 INFO @ Tue, 16 Jun 2020 10:43:45: 21000000 INFO @ Tue, 16 Jun 2020 10:43:46: 31000000 INFO @ Tue, 16 Jun 2020 10:43:49: 27000000 INFO @ Tue, 16 Jun 2020 10:43:52: 22000000 INFO @ Tue, 16 Jun 2020 10:43:52: 32000000 INFO @ Tue, 16 Jun 2020 10:43:55: 28000000 INFO @ Tue, 16 Jun 2020 10:43:58: 23000000 INFO @ Tue, 16 Jun 2020 10:43:58: 33000000 INFO @ Tue, 16 Jun 2020 10:44:01: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:44:04: 24000000 INFO @ Tue, 16 Jun 2020 10:44:04: 34000000 INFO @ Tue, 16 Jun 2020 10:44:08: 30000000 INFO @ Tue, 16 Jun 2020 10:44:10: 25000000 INFO @ Tue, 16 Jun 2020 10:44:10: 35000000 INFO @ Tue, 16 Jun 2020 10:44:12: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:44:12: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:44:12: #1 total tags in treatment: 6882082 INFO @ Tue, 16 Jun 2020 10:44:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:44:12: #1 tags after filtering in treatment: 2832961 INFO @ Tue, 16 Jun 2020 10:44:12: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 16 Jun 2020 10:44:12: #1 finished! INFO @ Tue, 16 Jun 2020 10:44:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:44:12: #2 number of paired peaks: 2502 INFO @ Tue, 16 Jun 2020 10:44:12: start model_add_line... INFO @ Tue, 16 Jun 2020 10:44:12: start X-correlation... INFO @ Tue, 16 Jun 2020 10:44:12: end of X-cor INFO @ Tue, 16 Jun 2020 10:44:12: #2 finished! INFO @ Tue, 16 Jun 2020 10:44:12: #2 predicted fragment length is 244 bps INFO @ Tue, 16 Jun 2020 10:44:12: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 16 Jun 2020 10:44:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.05_model.r INFO @ Tue, 16 Jun 2020 10:44:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:44:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:44:14: 31000000 INFO @ Tue, 16 Jun 2020 10:44:16: 26000000 INFO @ Tue, 16 Jun 2020 10:44:20: 32000000 INFO @ Tue, 16 Jun 2020 10:44:22: 27000000 INFO @ Tue, 16 Jun 2020 10:44:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:44:26: 33000000 INFO @ Tue, 16 Jun 2020 10:44:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:44:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:44:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.05_summits.bed INFO @ Tue, 16 Jun 2020 10:44:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3795 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:44:28: 28000000 INFO @ Tue, 16 Jun 2020 10:44:32: 34000000 INFO @ Tue, 16 Jun 2020 10:44:34: 29000000 INFO @ Tue, 16 Jun 2020 10:44:38: 35000000 INFO @ Tue, 16 Jun 2020 10:44:39: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:44:39: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:44:39: #1 total tags in treatment: 6882082 INFO @ Tue, 16 Jun 2020 10:44:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:44:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:44:39: #1 tags after filtering in treatment: 2832961 INFO @ Tue, 16 Jun 2020 10:44:39: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 16 Jun 2020 10:44:39: #1 finished! INFO @ Tue, 16 Jun 2020 10:44:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:44:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:44:40: #2 number of paired peaks: 2502 INFO @ Tue, 16 Jun 2020 10:44:40: start model_add_line... INFO @ Tue, 16 Jun 2020 10:44:40: start X-correlation... INFO @ Tue, 16 Jun 2020 10:44:40: end of X-cor INFO @ Tue, 16 Jun 2020 10:44:40: #2 finished! INFO @ Tue, 16 Jun 2020 10:44:40: #2 predicted fragment length is 244 bps INFO @ Tue, 16 Jun 2020 10:44:40: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 16 Jun 2020 10:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.10_model.r INFO @ Tue, 16 Jun 2020 10:44:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:44:40: 30000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:44:46: 31000000 INFO @ Tue, 16 Jun 2020 10:44:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:44:51: 32000000 INFO @ Tue, 16 Jun 2020 10:44:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.10_summits.bed INFO @ Tue, 16 Jun 2020 10:44:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2383 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:44:57: 33000000 INFO @ Tue, 16 Jun 2020 10:45:03: 34000000 INFO @ Tue, 16 Jun 2020 10:45:09: 35000000 INFO @ Tue, 16 Jun 2020 10:45:10: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:45:10: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:45:10: #1 total tags in treatment: 6882082 INFO @ Tue, 16 Jun 2020 10:45:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:45:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:45:10: #1 tags after filtering in treatment: 2832961 INFO @ Tue, 16 Jun 2020 10:45:10: #1 Redundant rate of treatment: 0.59 INFO @ Tue, 16 Jun 2020 10:45:10: #1 finished! INFO @ Tue, 16 Jun 2020 10:45:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:45:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:45:11: #2 number of paired peaks: 2502 INFO @ Tue, 16 Jun 2020 10:45:11: start model_add_line... INFO @ Tue, 16 Jun 2020 10:45:11: start X-correlation... INFO @ Tue, 16 Jun 2020 10:45:11: end of X-cor INFO @ Tue, 16 Jun 2020 10:45:11: #2 finished! INFO @ Tue, 16 Jun 2020 10:45:11: #2 predicted fragment length is 244 bps INFO @ Tue, 16 Jun 2020 10:45:11: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 16 Jun 2020 10:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.20_model.r INFO @ Tue, 16 Jun 2020 10:45:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:45:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:45:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012474/SRX4012474.20_summits.bed INFO @ Tue, 16 Jun 2020 10:45:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1322 records, 4 fields): 3 millis CompletedMACS2peakCalling