Job ID = 6367712 SRX = SRX4012476 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:50 prefetch.2.10.7: 1) Downloading 'SRR7082717'... 2020-06-15T23:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:10 prefetch.2.10.7: 1) 'SRR7082717' was downloaded successfully Read 32420082 spots for SRR7082717/SRR7082717.sra Written 32420082 spots for SRR7082717/SRR7082717.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: 01:19:27 32420082 reads; of these: 32420082 (100.00%) were paired; of these: 9004887 (27.78%) aligned concordantly 0 times 13149720 (40.56%) aligned concordantly exactly 1 time 10265475 (31.66%) aligned concordantly >1 times ---- 9004887 pairs aligned concordantly 0 times; of these: 617372 (6.86%) aligned discordantly 1 time ---- 8387515 pairs aligned 0 times concordantly or discordantly; of these: 16775030 mates make up the pairs; of these: 9453888 (56.36%) aligned 0 times 2050608 (12.22%) aligned exactly 1 time 5270534 (31.42%) aligned >1 times 85.42% overall alignment rate Time searching: 01:19:28 Overall time: 01:19:28 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 24 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] 4897490 / 23634227 = 0.2072 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 10:37:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.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 10:37:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:37:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:37:58: 1000000 INFO @ Tue, 16 Jun 2020 10:38:05: 2000000 INFO @ Tue, 16 Jun 2020 10:38:11: 3000000 INFO @ Tue, 16 Jun 2020 10:38:17: 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 10:38:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.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 10:38:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:38:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:38:24: 5000000 INFO @ Tue, 16 Jun 2020 10:38:29: 1000000 INFO @ Tue, 16 Jun 2020 10:38:32: 6000000 INFO @ Tue, 16 Jun 2020 10:38:36: 2000000 INFO @ Tue, 16 Jun 2020 10:38:39: 7000000 INFO @ Tue, 16 Jun 2020 10:38:43: 3000000 INFO @ Tue, 16 Jun 2020 10:38:46: 8000000 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 10:38:50: 4000000 INFO @ Tue, 16 Jun 2020 10:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.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 10:38:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:38:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:38:53: 9000000 INFO @ Tue, 16 Jun 2020 10:38:58: 5000000 INFO @ Tue, 16 Jun 2020 10:38:59: 1000000 INFO @ Tue, 16 Jun 2020 10:39:01: 10000000 INFO @ Tue, 16 Jun 2020 10:39:05: 6000000 INFO @ Tue, 16 Jun 2020 10:39:06: 2000000 INFO @ Tue, 16 Jun 2020 10:39:08: 11000000 INFO @ Tue, 16 Jun 2020 10:39:13: 7000000 INFO @ Tue, 16 Jun 2020 10:39:14: 3000000 INFO @ Tue, 16 Jun 2020 10:39:16: 12000000 INFO @ Tue, 16 Jun 2020 10:39:21: 8000000 INFO @ Tue, 16 Jun 2020 10:39:21: 4000000 INFO @ Tue, 16 Jun 2020 10:39:24: 13000000 INFO @ Tue, 16 Jun 2020 10:39:28: 9000000 INFO @ Tue, 16 Jun 2020 10:39:28: 5000000 INFO @ Tue, 16 Jun 2020 10:39:31: 14000000 INFO @ Tue, 16 Jun 2020 10:39:36: 10000000 INFO @ Tue, 16 Jun 2020 10:39:36: 6000000 INFO @ Tue, 16 Jun 2020 10:39:39: 15000000 INFO @ Tue, 16 Jun 2020 10:39:43: 11000000 INFO @ Tue, 16 Jun 2020 10:39:44: 7000000 INFO @ Tue, 16 Jun 2020 10:39:46: 16000000 INFO @ Tue, 16 Jun 2020 10:39:51: 12000000 INFO @ Tue, 16 Jun 2020 10:39:51: 8000000 INFO @ Tue, 16 Jun 2020 10:39:54: 17000000 INFO @ Tue, 16 Jun 2020 10:39:59: 13000000 INFO @ Tue, 16 Jun 2020 10:39:59: 9000000 INFO @ Tue, 16 Jun 2020 10:40:01: 18000000 INFO @ Tue, 16 Jun 2020 10:40:06: 14000000 INFO @ Tue, 16 Jun 2020 10:40:06: 10000000 INFO @ Tue, 16 Jun 2020 10:40:09: 19000000 INFO @ Tue, 16 Jun 2020 10:40:14: 15000000 INFO @ Tue, 16 Jun 2020 10:40:14: 11000000 INFO @ Tue, 16 Jun 2020 10:40:17: 20000000 INFO @ Tue, 16 Jun 2020 10:40:21: 16000000 INFO @ Tue, 16 Jun 2020 10:40:22: 12000000 INFO @ Tue, 16 Jun 2020 10:40:25: 21000000 INFO @ Tue, 16 Jun 2020 10:40:29: 17000000 INFO @ Tue, 16 Jun 2020 10:40:29: 13000000 INFO @ Tue, 16 Jun 2020 10:40:32: 22000000 INFO @ Tue, 16 Jun 2020 10:40:37: 18000000 INFO @ Tue, 16 Jun 2020 10:40:37: 14000000 INFO @ Tue, 16 Jun 2020 10:40:40: 23000000 INFO @ Tue, 16 Jun 2020 10:40:45: 19000000 INFO @ Tue, 16 Jun 2020 10:40:45: 15000000 INFO @ Tue, 16 Jun 2020 10:40:48: 24000000 INFO @ Tue, 16 Jun 2020 10:40:52: 20000000 INFO @ Tue, 16 Jun 2020 10:40:53: 16000000 INFO @ Tue, 16 Jun 2020 10:40:56: 25000000 INFO @ Tue, 16 Jun 2020 10:41:00: 21000000 INFO @ Tue, 16 Jun 2020 10:41:01: 17000000 INFO @ Tue, 16 Jun 2020 10:41:04: 26000000 INFO @ Tue, 16 Jun 2020 10:41:08: 22000000 INFO @ Tue, 16 Jun 2020 10:41:09: 18000000 INFO @ Tue, 16 Jun 2020 10:41:12: 27000000 INFO @ Tue, 16 Jun 2020 10:41:16: 23000000 INFO @ Tue, 16 Jun 2020 10:41:17: 19000000 INFO @ Tue, 16 Jun 2020 10:41:19: 28000000 INFO @ Tue, 16 Jun 2020 10:41:23: 24000000 INFO @ Tue, 16 Jun 2020 10:41:24: 20000000 INFO @ Tue, 16 Jun 2020 10:41:27: 29000000 INFO @ Tue, 16 Jun 2020 10:41:31: 25000000 INFO @ Tue, 16 Jun 2020 10:41:32: 21000000 INFO @ Tue, 16 Jun 2020 10:41:35: 30000000 INFO @ Tue, 16 Jun 2020 10:41:39: 26000000 INFO @ Tue, 16 Jun 2020 10:41:40: 22000000 INFO @ Tue, 16 Jun 2020 10:41:43: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:41:47: 27000000 INFO @ Tue, 16 Jun 2020 10:41:48: 23000000 INFO @ Tue, 16 Jun 2020 10:41:50: 32000000 INFO @ Tue, 16 Jun 2020 10:41:54: 28000000 INFO @ Tue, 16 Jun 2020 10:41:56: 24000000 INFO @ Tue, 16 Jun 2020 10:41:58: 33000000 INFO @ Tue, 16 Jun 2020 10:42:02: 29000000 INFO @ Tue, 16 Jun 2020 10:42:03: 25000000 INFO @ Tue, 16 Jun 2020 10:42:06: 34000000 INFO @ Tue, 16 Jun 2020 10:42:10: 30000000 INFO @ Tue, 16 Jun 2020 10:42:11: 26000000 INFO @ Tue, 16 Jun 2020 10:42:14: 35000000 INFO @ Tue, 16 Jun 2020 10:42:17: 31000000 INFO @ Tue, 16 Jun 2020 10:42:19: 27000000 INFO @ Tue, 16 Jun 2020 10:42:22: 36000000 INFO @ Tue, 16 Jun 2020 10:42:25: 32000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:42:27: 28000000 INFO @ Tue, 16 Jun 2020 10:42:29: 37000000 INFO @ Tue, 16 Jun 2020 10:42:33: 33000000 INFO @ Tue, 16 Jun 2020 10:42:34: 29000000 INFO @ Tue, 16 Jun 2020 10:42:37: 38000000 INFO @ Tue, 16 Jun 2020 10:42:40: 34000000 INFO @ Tue, 16 Jun 2020 10:42:42: 30000000 INFO @ Tue, 16 Jun 2020 10:42:44: 39000000 INFO @ Tue, 16 Jun 2020 10:42:48: 35000000 INFO @ Tue, 16 Jun 2020 10:42:50: 31000000 INFO @ Tue, 16 Jun 2020 10:42:52: 40000000 INFO @ Tue, 16 Jun 2020 10:42:56: 36000000 INFO @ Tue, 16 Jun 2020 10:42:57: 32000000 INFO @ Tue, 16 Jun 2020 10:43:00: 41000000 INFO @ Tue, 16 Jun 2020 10:43:04: 37000000 INFO @ Tue, 16 Jun 2020 10:43:05: 33000000 INFO @ Tue, 16 Jun 2020 10:43:08: 42000000 INFO @ Tue, 16 Jun 2020 10:43:11: 38000000 INFO @ Tue, 16 Jun 2020 10:43:13: 34000000 INFO @ Tue, 16 Jun 2020 10:43:16: 43000000 INFO @ Tue, 16 Jun 2020 10:43:19: 39000000 INFO @ Tue, 16 Jun 2020 10:43:21: 35000000 INFO @ Tue, 16 Jun 2020 10:43:24: 44000000 INFO @ Tue, 16 Jun 2020 10:43:27: 40000000 INFO @ Tue, 16 Jun 2020 10:43:29: 36000000 INFO @ Tue, 16 Jun 2020 10:43:31: 45000000 INFO @ Tue, 16 Jun 2020 10:43:35: 41000000 INFO @ Tue, 16 Jun 2020 10:43:36: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:43:36: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:43:36: #1 total tags in treatment: 18548324 INFO @ Tue, 16 Jun 2020 10:43:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:43:36: #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 10:43:37: #1 tags after filtering in treatment: 8400954 INFO @ Tue, 16 Jun 2020 10:43:37: #1 Redundant rate of treatment: 0.55 INFO @ Tue, 16 Jun 2020 10:43:37: #1 finished! INFO @ Tue, 16 Jun 2020 10:43:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:43:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:43:37: 37000000 INFO @ Tue, 16 Jun 2020 10:43:38: #2 number of paired peaks: 5031 INFO @ Tue, 16 Jun 2020 10:43:38: start model_add_line... INFO @ Tue, 16 Jun 2020 10:43:38: start X-correlation... INFO @ Tue, 16 Jun 2020 10:43:38: end of X-cor INFO @ Tue, 16 Jun 2020 10:43:38: #2 finished! INFO @ Tue, 16 Jun 2020 10:43:38: #2 predicted fragment length is 366 bps INFO @ Tue, 16 Jun 2020 10:43:38: #2 alternative fragment length(s) may be 366 bps INFO @ Tue, 16 Jun 2020 10:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.05_model.r INFO @ Tue, 16 Jun 2020 10:43:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:43:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:43:43: 42000000 INFO @ Tue, 16 Jun 2020 10:43:45: 38000000 INFO @ Tue, 16 Jun 2020 10:43:50: 43000000 INFO @ Tue, 16 Jun 2020 10:43:53: 39000000 INFO @ Tue, 16 Jun 2020 10:43:58: 44000000 INFO @ Tue, 16 Jun 2020 10:44:01: 40000000 INFO @ Tue, 16 Jun 2020 10:44:06: 45000000 INFO @ Tue, 16 Jun 2020 10:44:09: 41000000 INFO @ Tue, 16 Jun 2020 10:44:11: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:44:11: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:44:11: #1 total tags in treatment: 18548324 INFO @ Tue, 16 Jun 2020 10:44:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:44:11: #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 10:44:11: #1 tags after filtering in treatment: 8400954 INFO @ Tue, 16 Jun 2020 10:44:11: #1 Redundant rate of treatment: 0.55 INFO @ Tue, 16 Jun 2020 10:44:11: #1 finished! INFO @ Tue, 16 Jun 2020 10:44:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:44:12: #2 number of paired peaks: 5031 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 366 bps INFO @ Tue, 16 Jun 2020 10:44:12: #2 alternative fragment length(s) may be 366 bps INFO @ Tue, 16 Jun 2020 10:44:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.10_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 10:44:16: 42000000 INFO @ Tue, 16 Jun 2020 10:44:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:44:24: 43000000 INFO @ Tue, 16 Jun 2020 10:44:31: 44000000 INFO @ Tue, 16 Jun 2020 10:44:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:44:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:44:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.05_summits.bed INFO @ Tue, 16 Jun 2020 10:44:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6187 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:44:39: 45000000 INFO @ Tue, 16 Jun 2020 10:44:43: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:44:43: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:44:43: #1 total tags in treatment: 18548324 INFO @ Tue, 16 Jun 2020 10:44:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:44:43: #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 10:44:44: #1 tags after filtering in treatment: 8400954 INFO @ Tue, 16 Jun 2020 10:44:44: #1 Redundant rate of treatment: 0.55 INFO @ Tue, 16 Jun 2020 10:44:44: #1 finished! INFO @ Tue, 16 Jun 2020 10:44:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:44:45: #2 number of paired peaks: 5031 INFO @ Tue, 16 Jun 2020 10:44:45: start model_add_line... INFO @ Tue, 16 Jun 2020 10:44:45: start X-correlation... INFO @ Tue, 16 Jun 2020 10:44:45: end of X-cor INFO @ Tue, 16 Jun 2020 10:44:45: #2 finished! INFO @ Tue, 16 Jun 2020 10:44:45: #2 predicted fragment length is 366 bps INFO @ Tue, 16 Jun 2020 10:44:45: #2 alternative fragment length(s) may be 366 bps INFO @ Tue, 16 Jun 2020 10:44:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.20_model.r INFO @ Tue, 16 Jun 2020 10:44:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:44:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:44:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:45:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:45:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:45:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.10_summits.bed INFO @ Tue, 16 Jun 2020 10:45:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4934 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:45:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:45:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:45:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:45:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4012476/SRX4012476.20_summits.bed INFO @ Tue, 16 Jun 2020 10:45:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3892 records, 4 fields): 6 millis CompletedMACS2peakCalling