Job ID = 6367716 SRX = SRX4012480 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:32:35 prefetch.2.10.7: 1) Downloading 'SRR7082721'... 2020-06-15T23:32:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:12 prefetch.2.10.7: 1) 'SRR7082721' was downloaded successfully Read 37002202 spots for SRR7082721/SRR7082721.sra Written 37002202 spots for SRR7082721/SRR7082721.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:11:04 37002202 reads; of these: 37002202 (100.00%) were paired; of these: 11020878 (29.78%) aligned concordantly 0 times 16648638 (44.99%) aligned concordantly exactly 1 time 9332686 (25.22%) aligned concordantly >1 times ---- 11020878 pairs aligned concordantly 0 times; of these: 700067 (6.35%) aligned discordantly 1 time ---- 10320811 pairs aligned 0 times concordantly or discordantly; of these: 20641622 mates make up the pairs; of these: 14071259 (68.17%) aligned 0 times 1724108 (8.35%) aligned exactly 1 time 4846255 (23.48%) aligned >1 times 80.99% overall alignment rate Time searching: 01:11:05 Overall time: 01:11:05 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 28 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] 9838624 / 26274761 = 0.3745 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 10:29:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.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 10:29:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:29:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:29:19: 1000000 INFO @ Tue, 16 Jun 2020 10:29:27: 2000000 INFO @ Tue, 16 Jun 2020 10:29:35: 3000000 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 10:29:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.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 10:29:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:29:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:29:43: 4000000 INFO @ Tue, 16 Jun 2020 10:29:49: 1000000 INFO @ Tue, 16 Jun 2020 10:29:52: 5000000 INFO @ Tue, 16 Jun 2020 10:29:57: 2000000 INFO @ Tue, 16 Jun 2020 10:30:01: 6000000 INFO @ Tue, 16 Jun 2020 10:30:06: 3000000 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 10:30:09: 7000000 INFO @ Tue, 16 Jun 2020 10:30:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.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 10:30:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:30:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:30:14: 4000000 INFO @ Tue, 16 Jun 2020 10:30:19: 8000000 INFO @ Tue, 16 Jun 2020 10:30:19: 1000000 INFO @ Tue, 16 Jun 2020 10:30:23: 5000000 INFO @ Tue, 16 Jun 2020 10:30:28: 2000000 INFO @ Tue, 16 Jun 2020 10:30:28: 9000000 INFO @ Tue, 16 Jun 2020 10:30:32: 6000000 INFO @ Tue, 16 Jun 2020 10:30:37: 3000000 INFO @ Tue, 16 Jun 2020 10:30:37: 10000000 INFO @ Tue, 16 Jun 2020 10:30:41: 7000000 INFO @ Tue, 16 Jun 2020 10:30:46: 4000000 INFO @ Tue, 16 Jun 2020 10:30:46: 11000000 INFO @ Tue, 16 Jun 2020 10:30:50: 8000000 INFO @ Tue, 16 Jun 2020 10:30:55: 5000000 INFO @ Tue, 16 Jun 2020 10:30:55: 12000000 INFO @ Tue, 16 Jun 2020 10:30:59: 9000000 INFO @ Tue, 16 Jun 2020 10:31:04: 6000000 INFO @ Tue, 16 Jun 2020 10:31:04: 13000000 INFO @ Tue, 16 Jun 2020 10:31:08: 10000000 INFO @ Tue, 16 Jun 2020 10:31:13: 14000000 INFO @ Tue, 16 Jun 2020 10:31:13: 7000000 INFO @ Tue, 16 Jun 2020 10:31:16: 11000000 INFO @ Tue, 16 Jun 2020 10:31:21: 15000000 INFO @ Tue, 16 Jun 2020 10:31:22: 8000000 INFO @ Tue, 16 Jun 2020 10:31:25: 12000000 INFO @ Tue, 16 Jun 2020 10:31:31: 16000000 INFO @ Tue, 16 Jun 2020 10:31:31: 9000000 INFO @ Tue, 16 Jun 2020 10:31:34: 13000000 INFO @ Tue, 16 Jun 2020 10:31:40: 17000000 INFO @ Tue, 16 Jun 2020 10:31:40: 10000000 INFO @ Tue, 16 Jun 2020 10:31:43: 14000000 INFO @ Tue, 16 Jun 2020 10:31:49: 18000000 INFO @ Tue, 16 Jun 2020 10:31:49: 11000000 INFO @ Tue, 16 Jun 2020 10:31:51: 15000000 INFO @ Tue, 16 Jun 2020 10:31:58: 19000000 INFO @ Tue, 16 Jun 2020 10:31:58: 12000000 INFO @ Tue, 16 Jun 2020 10:32:00: 16000000 INFO @ Tue, 16 Jun 2020 10:32:07: 20000000 INFO @ Tue, 16 Jun 2020 10:32:07: 13000000 INFO @ Tue, 16 Jun 2020 10:32:09: 17000000 INFO @ Tue, 16 Jun 2020 10:32:16: 21000000 INFO @ Tue, 16 Jun 2020 10:32:17: 14000000 INFO @ Tue, 16 Jun 2020 10:32:18: 18000000 INFO @ Tue, 16 Jun 2020 10:32:25: 22000000 INFO @ Tue, 16 Jun 2020 10:32:26: 15000000 INFO @ Tue, 16 Jun 2020 10:32:27: 19000000 INFO @ Tue, 16 Jun 2020 10:32:35: 23000000 INFO @ Tue, 16 Jun 2020 10:32:35: 16000000 INFO @ Tue, 16 Jun 2020 10:32:36: 20000000 INFO @ Tue, 16 Jun 2020 10:32:44: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:32:44: 24000000 INFO @ Tue, 16 Jun 2020 10:32:45: 21000000 INFO @ Tue, 16 Jun 2020 10:32:54: 18000000 INFO @ Tue, 16 Jun 2020 10:32:54: 25000000 INFO @ Tue, 16 Jun 2020 10:32:54: 22000000 INFO @ Tue, 16 Jun 2020 10:33:03: 19000000 INFO @ Tue, 16 Jun 2020 10:33:03: 26000000 INFO @ Tue, 16 Jun 2020 10:33:04: 23000000 INFO @ Tue, 16 Jun 2020 10:33:12: 20000000 INFO @ Tue, 16 Jun 2020 10:33:12: 27000000 INFO @ Tue, 16 Jun 2020 10:33:13: 24000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:33:21: 21000000 INFO @ Tue, 16 Jun 2020 10:33:21: 28000000 INFO @ Tue, 16 Jun 2020 10:33:22: 25000000 INFO @ Tue, 16 Jun 2020 10:33:30: 22000000 INFO @ Tue, 16 Jun 2020 10:33:30: 29000000 INFO @ Tue, 16 Jun 2020 10:33:31: 26000000 INFO @ Tue, 16 Jun 2020 10:33:40: 30000000 INFO @ Tue, 16 Jun 2020 10:33:40: 23000000 INFO @ Tue, 16 Jun 2020 10:33:40: 27000000 INFO @ Tue, 16 Jun 2020 10:33:49: 31000000 INFO @ Tue, 16 Jun 2020 10:33:49: 28000000 INFO @ Tue, 16 Jun 2020 10:33:49: 24000000 INFO @ Tue, 16 Jun 2020 10:33:58: 29000000 INFO @ Tue, 16 Jun 2020 10:33:58: 32000000 INFO @ Tue, 16 Jun 2020 10:33:59: 25000000 INFO @ Tue, 16 Jun 2020 10:34:07: 30000000 INFO @ Tue, 16 Jun 2020 10:34:07: 33000000 INFO @ Tue, 16 Jun 2020 10:34:08: 26000000 INFO @ Tue, 16 Jun 2020 10:34:16: 31000000 INFO @ Tue, 16 Jun 2020 10:34:17: 34000000 INFO @ Tue, 16 Jun 2020 10:34:17: 27000000 INFO @ Tue, 16 Jun 2020 10:34:24: 32000000 INFO @ Tue, 16 Jun 2020 10:34:26: 28000000 INFO @ Tue, 16 Jun 2020 10:34:26: 35000000 INFO @ Tue, 16 Jun 2020 10:34:33: 33000000 INFO @ Tue, 16 Jun 2020 10:34:36: 29000000 INFO @ Tue, 16 Jun 2020 10:34:36: 36000000 INFO @ Tue, 16 Jun 2020 10:34:42: 34000000 INFO @ Tue, 16 Jun 2020 10:34:45: 30000000 INFO @ Tue, 16 Jun 2020 10:34:45: 37000000 INFO @ Tue, 16 Jun 2020 10:34:51: 35000000 INFO @ Tue, 16 Jun 2020 10:34:54: 31000000 INFO @ Tue, 16 Jun 2020 10:34:55: 38000000 INFO @ Tue, 16 Jun 2020 10:35:00: 36000000 INFO @ Tue, 16 Jun 2020 10:35:03: 32000000 INFO @ Tue, 16 Jun 2020 10:35:03: 39000000 INFO @ Tue, 16 Jun 2020 10:35:09: 37000000 INFO @ Tue, 16 Jun 2020 10:35:12: 40000000 INFO @ Tue, 16 Jun 2020 10:35:13: 33000000 INFO @ Tue, 16 Jun 2020 10:35:15: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:35:15: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:35:15: #1 total tags in treatment: 16224739 INFO @ Tue, 16 Jun 2020 10:35:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:35:15: #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 10:35:15: #1 tags after filtering in treatment: 7078334 INFO @ Tue, 16 Jun 2020 10:35:15: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 16 Jun 2020 10:35:15: #1 finished! INFO @ Tue, 16 Jun 2020 10:35:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:35:16: #2 number of paired peaks: 6770 INFO @ Tue, 16 Jun 2020 10:35:16: start model_add_line... INFO @ Tue, 16 Jun 2020 10:35:16: start X-correlation... INFO @ Tue, 16 Jun 2020 10:35:16: end of X-cor INFO @ Tue, 16 Jun 2020 10:35:16: #2 finished! INFO @ Tue, 16 Jun 2020 10:35:16: #2 predicted fragment length is 342 bps INFO @ Tue, 16 Jun 2020 10:35:16: #2 alternative fragment length(s) may be 342 bps INFO @ Tue, 16 Jun 2020 10:35:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.05_model.r INFO @ Tue, 16 Jun 2020 10:35:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:35:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:35:17: 38000000 INFO @ Tue, 16 Jun 2020 10:35:22: 34000000 INFO @ Tue, 16 Jun 2020 10:35:25: 39000000 INFO @ Tue, 16 Jun 2020 10:35:31: 35000000 INFO @ Tue, 16 Jun 2020 10:35:33: 40000000 INFO @ Tue, 16 Jun 2020 10:35:36: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:35:36: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:35:36: #1 total tags in treatment: 16224739 INFO @ Tue, 16 Jun 2020 10:35:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:35:36: #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 10:35:36: #1 tags after filtering in treatment: 7078334 INFO @ Tue, 16 Jun 2020 10:35:36: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 16 Jun 2020 10:35:36: #1 finished! INFO @ Tue, 16 Jun 2020 10:35:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:35:37: #2 number of paired peaks: 6770 INFO @ Tue, 16 Jun 2020 10:35:37: start model_add_line... INFO @ Tue, 16 Jun 2020 10:35:37: start X-correlation... INFO @ Tue, 16 Jun 2020 10:35:37: end of X-cor INFO @ Tue, 16 Jun 2020 10:35:37: #2 finished! INFO @ Tue, 16 Jun 2020 10:35:37: #2 predicted fragment length is 342 bps INFO @ Tue, 16 Jun 2020 10:35:37: #2 alternative fragment length(s) may be 342 bps INFO @ Tue, 16 Jun 2020 10:35:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.10_model.r INFO @ Tue, 16 Jun 2020 10:35:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:35:39: 36000000 INFO @ Tue, 16 Jun 2020 10:35:47: 37000000 INFO @ Tue, 16 Jun 2020 10:35:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:35:55: 38000000 INFO @ Tue, 16 Jun 2020 10:36:03: 39000000 INFO @ Tue, 16 Jun 2020 10:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:36:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.05_summits.bed INFO @ Tue, 16 Jun 2020 10:36:06: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7374 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:36:11: 40000000 INFO @ Tue, 16 Jun 2020 10:36:13: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:36:13: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:36:13: #1 total tags in treatment: 16224739 INFO @ Tue, 16 Jun 2020 10:36:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:36:13: #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 10:36:13: #1 tags after filtering in treatment: 7078334 INFO @ Tue, 16 Jun 2020 10:36:13: #1 Redundant rate of treatment: 0.56 INFO @ Tue, 16 Jun 2020 10:36:13: #1 finished! INFO @ Tue, 16 Jun 2020 10:36:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:36:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:36:14: #2 number of paired peaks: 6770 INFO @ Tue, 16 Jun 2020 10:36:14: start model_add_line... INFO @ Tue, 16 Jun 2020 10:36:14: start X-correlation... INFO @ Tue, 16 Jun 2020 10:36:14: end of X-cor INFO @ Tue, 16 Jun 2020 10:36:14: #2 finished! INFO @ Tue, 16 Jun 2020 10:36:14: #2 predicted fragment length is 342 bps INFO @ Tue, 16 Jun 2020 10:36:14: #2 alternative fragment length(s) may be 342 bps INFO @ Tue, 16 Jun 2020 10:36:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.20_model.r INFO @ Tue, 16 Jun 2020 10:36:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:36:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:36:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.10_summits.bed INFO @ Tue, 16 Jun 2020 10:36:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6274 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:36:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012480/SRX4012480.20_summits.bed INFO @ Tue, 16 Jun 2020 10:37:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5291 records, 4 fields): 7 millis CompletedMACS2peakCalling