Job ID = 6497382 SRX = SRX4085362 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:11:36 prefetch.2.10.7: 1) Downloading 'SRR7167391'... 2020-06-25T22:11:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:16:04 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:16:04 prefetch.2.10.7: 1) 'SRR7167391' was downloaded successfully Read 17406003 spots for SRR7167391/SRR7167391.sra Written 17406003 spots for SRR7167391/SRR7167391.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: 00:14:41 17406003 reads; of these: 17406003 (100.00%) were paired; of these: 496165 (2.85%) aligned concordantly 0 times 14908928 (85.65%) aligned concordantly exactly 1 time 2000910 (11.50%) aligned concordantly >1 times ---- 496165 pairs aligned concordantly 0 times; of these: 125802 (25.35%) aligned discordantly 1 time ---- 370363 pairs aligned 0 times concordantly or discordantly; of these: 740726 mates make up the pairs; of these: 398190 (53.76%) aligned 0 times 256662 (34.65%) aligned exactly 1 time 85874 (11.59%) aligned >1 times 98.86% overall alignment rate Time searching: 00:14:42 Overall time: 00:14:42 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 16 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] 1826434 / 16971506 = 0.1076 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, 26 Jun 2020 07:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.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 @ Fri, 26 Jun 2020 07:43:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:43:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:43:10: 1000000 INFO @ Fri, 26 Jun 2020 07:43:16: 2000000 INFO @ Fri, 26 Jun 2020 07:43:22: 3000000 INFO @ Fri, 26 Jun 2020 07:43:28: 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 @ Fri, 26 Jun 2020 07:43:34: 5000000 INFO @ Fri, 26 Jun 2020 07:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.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 @ Fri, 26 Jun 2020 07:43:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:43:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:43:40: 6000000 INFO @ Fri, 26 Jun 2020 07:43:42: 1000000 INFO @ Fri, 26 Jun 2020 07:43:47: 7000000 INFO @ Fri, 26 Jun 2020 07:43:48: 2000000 INFO @ Fri, 26 Jun 2020 07:43:53: 8000000 INFO @ Fri, 26 Jun 2020 07:43:55: 3000000 INFO @ Fri, 26 Jun 2020 07:44:00: 9000000 INFO @ Fri, 26 Jun 2020 07:44:01: 4000000 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, 26 Jun 2020 07:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.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 @ Fri, 26 Jun 2020 07:44:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:44:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:44:07: 10000000 INFO @ Fri, 26 Jun 2020 07:44:08: 5000000 INFO @ Fri, 26 Jun 2020 07:44:11: 1000000 INFO @ Fri, 26 Jun 2020 07:44:13: 11000000 INFO @ Fri, 26 Jun 2020 07:44:14: 6000000 INFO @ Fri, 26 Jun 2020 07:44:18: 2000000 INFO @ Fri, 26 Jun 2020 07:44:20: 12000000 INFO @ Fri, 26 Jun 2020 07:44:21: 7000000 INFO @ Fri, 26 Jun 2020 07:44:25: 3000000 INFO @ Fri, 26 Jun 2020 07:44:27: 13000000 INFO @ Fri, 26 Jun 2020 07:44:28: 8000000 INFO @ Fri, 26 Jun 2020 07:44:32: 4000000 INFO @ Fri, 26 Jun 2020 07:44:34: 14000000 INFO @ Fri, 26 Jun 2020 07:44:34: 9000000 INFO @ Fri, 26 Jun 2020 07:44:39: 5000000 INFO @ Fri, 26 Jun 2020 07:44:41: 15000000 INFO @ Fri, 26 Jun 2020 07:44:41: 10000000 INFO @ Fri, 26 Jun 2020 07:44:45: 6000000 INFO @ Fri, 26 Jun 2020 07:44:48: 16000000 INFO @ Fri, 26 Jun 2020 07:44:48: 11000000 INFO @ Fri, 26 Jun 2020 07:44:52: 7000000 INFO @ Fri, 26 Jun 2020 07:44:54: 17000000 INFO @ Fri, 26 Jun 2020 07:44:55: 12000000 INFO @ Fri, 26 Jun 2020 07:44:59: 8000000 INFO @ Fri, 26 Jun 2020 07:45:01: 18000000 INFO @ Fri, 26 Jun 2020 07:45:02: 13000000 INFO @ Fri, 26 Jun 2020 07:45:06: 9000000 INFO @ Fri, 26 Jun 2020 07:45:08: 19000000 INFO @ Fri, 26 Jun 2020 07:45:08: 14000000 INFO @ Fri, 26 Jun 2020 07:45:13: 10000000 INFO @ Fri, 26 Jun 2020 07:45:15: 20000000 INFO @ Fri, 26 Jun 2020 07:45:15: 15000000 INFO @ Fri, 26 Jun 2020 07:45:19: 11000000 INFO @ Fri, 26 Jun 2020 07:45:21: 21000000 INFO @ Fri, 26 Jun 2020 07:45:22: 16000000 INFO @ Fri, 26 Jun 2020 07:45:26: 12000000 INFO @ Fri, 26 Jun 2020 07:45:28: 22000000 INFO @ Fri, 26 Jun 2020 07:45:28: 17000000 INFO @ Fri, 26 Jun 2020 07:45:32: 13000000 INFO @ Fri, 26 Jun 2020 07:45:35: 23000000 INFO @ Fri, 26 Jun 2020 07:45:35: 18000000 INFO @ Fri, 26 Jun 2020 07:45:39: 14000000 INFO @ Fri, 26 Jun 2020 07:45:41: 24000000 INFO @ Fri, 26 Jun 2020 07:45:41: 19000000 INFO @ Fri, 26 Jun 2020 07:45:46: 15000000 INFO @ Fri, 26 Jun 2020 07:45:48: 25000000 INFO @ Fri, 26 Jun 2020 07:45:48: 20000000 INFO @ Fri, 26 Jun 2020 07:45:52: 16000000 INFO @ Fri, 26 Jun 2020 07:45:54: 26000000 INFO @ Fri, 26 Jun 2020 07:45:55: 21000000 INFO @ Fri, 26 Jun 2020 07:45:59: 17000000 INFO @ Fri, 26 Jun 2020 07:46:01: 27000000 INFO @ Fri, 26 Jun 2020 07:46:01: 22000000 INFO @ Fri, 26 Jun 2020 07:46:05: 18000000 INFO @ Fri, 26 Jun 2020 07:46:08: 28000000 INFO @ Fri, 26 Jun 2020 07:46:08: 23000000 INFO @ Fri, 26 Jun 2020 07:46:12: 19000000 INFO @ Fri, 26 Jun 2020 07:46:14: 29000000 INFO @ Fri, 26 Jun 2020 07:46:14: 24000000 INFO @ Fri, 26 Jun 2020 07:46:18: 20000000 INFO @ Fri, 26 Jun 2020 07:46:21: 30000000 INFO @ Fri, 26 Jun 2020 07:46:21: 25000000 INFO @ Fri, 26 Jun 2020 07:46:25: 21000000 INFO @ Fri, 26 Jun 2020 07:46:26: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:46:26: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:46:26: #1 total tags in treatment: 15086911 INFO @ Fri, 26 Jun 2020 07:46:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:46:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:46:26: #1 tags after filtering in treatment: 13334920 INFO @ Fri, 26 Jun 2020 07:46:26: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 07:46:26: #1 finished! INFO @ Fri, 26 Jun 2020 07:46:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:46:27: #2 number of paired peaks: 157 WARNING @ Fri, 26 Jun 2020 07:46:27: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 26 Jun 2020 07:46:27: start model_add_line... INFO @ Fri, 26 Jun 2020 07:46:27: start X-correlation... INFO @ Fri, 26 Jun 2020 07:46:27: end of X-cor INFO @ Fri, 26 Jun 2020 07:46:27: #2 finished! INFO @ Fri, 26 Jun 2020 07:46:27: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 07:46:27: #2 alternative fragment length(s) may be 3,123,147 bps INFO @ Fri, 26 Jun 2020 07:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.05_model.r INFO @ Fri, 26 Jun 2020 07:46:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:46:27: 26000000 INFO @ Fri, 26 Jun 2020 07:46:31: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:46:34: 27000000 INFO @ Fri, 26 Jun 2020 07:46:38: 23000000 INFO @ Fri, 26 Jun 2020 07:46:41: 28000000 INFO @ Fri, 26 Jun 2020 07:46:44: 24000000 INFO @ Fri, 26 Jun 2020 07:46:47: 29000000 INFO @ Fri, 26 Jun 2020 07:46:51: 25000000 INFO @ Fri, 26 Jun 2020 07:46:53: 30000000 INFO @ Fri, 26 Jun 2020 07:46:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:46:57: 26000000 INFO @ Fri, 26 Jun 2020 07:46:58: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:46:58: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:46:58: #1 total tags in treatment: 15086911 INFO @ Fri, 26 Jun 2020 07:46:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:46:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:46:59: #1 tags after filtering in treatment: 13334920 INFO @ Fri, 26 Jun 2020 07:46:59: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 07:46:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:46:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:46:59: #2 number of paired peaks: 157 WARNING @ Fri, 26 Jun 2020 07:46:59: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 26 Jun 2020 07:46:59: start model_add_line... INFO @ Fri, 26 Jun 2020 07:46:59: start X-correlation... INFO @ Fri, 26 Jun 2020 07:46:59: end of X-cor INFO @ Fri, 26 Jun 2020 07:46:59: #2 finished! INFO @ Fri, 26 Jun 2020 07:46:59: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 07:46:59: #2 alternative fragment length(s) may be 3,123,147 bps INFO @ Fri, 26 Jun 2020 07:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.10_model.r INFO @ Fri, 26 Jun 2020 07:47:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:47:03: 27000000 INFO @ Fri, 26 Jun 2020 07:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.05_summits.bed INFO @ Fri, 26 Jun 2020 07:47:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (822 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:47:09: 28000000 INFO @ Fri, 26 Jun 2020 07:47:15: 29000000 INFO @ Fri, 26 Jun 2020 07:47:21: 30000000 INFO @ Fri, 26 Jun 2020 07:47:25: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:47:25: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:47:25: #1 total tags in treatment: 15086911 INFO @ Fri, 26 Jun 2020 07:47:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:47:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:47:26: #1 tags after filtering in treatment: 13334920 INFO @ Fri, 26 Jun 2020 07:47:26: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 07:47:26: #1 finished! INFO @ Fri, 26 Jun 2020 07:47:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:47:26: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:47:26: #2 number of paired peaks: 157 WARNING @ Fri, 26 Jun 2020 07:47:26: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 26 Jun 2020 07:47:26: start model_add_line... INFO @ Fri, 26 Jun 2020 07:47:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:47:27: start X-correlation... INFO @ Fri, 26 Jun 2020 07:47:27: end of X-cor INFO @ Fri, 26 Jun 2020 07:47:27: #2 finished! INFO @ Fri, 26 Jun 2020 07:47:27: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 07:47:27: #2 alternative fragment length(s) may be 3,123,147 bps INFO @ Fri, 26 Jun 2020 07:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.20_model.r INFO @ Fri, 26 Jun 2020 07:47:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.10_summits.bed INFO @ Fri, 26 Jun 2020 07:47:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (280 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:47:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085362/SRX4085362.20_summits.bed INFO @ Fri, 26 Jun 2020 07:48:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (127 records, 4 fields): 2 millis CompletedMACS2peakCalling