Job ID = 6507766 SRX = SRX4085349 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T12:47:47 prefetch.2.10.7: 1) Downloading 'SRR7167378'... 2020-06-26T12:47:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:56:01 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:56:01 prefetch.2.10.7: 1) 'SRR7167378' was downloaded successfully Read 36867961 spots for SRR7167378/SRR7167378.sra Written 36867961 spots for SRR7167378/SRR7167378.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: 00:29:29 36867961 reads; of these: 36867961 (100.00%) were paired; of these: 6861939 (18.61%) aligned concordantly 0 times 26268981 (71.25%) aligned concordantly exactly 1 time 3737041 (10.14%) aligned concordantly >1 times ---- 6861939 pairs aligned concordantly 0 times; of these: 1279467 (18.65%) aligned discordantly 1 time ---- 5582472 pairs aligned 0 times concordantly or discordantly; of these: 11164944 mates make up the pairs; of these: 7529681 (67.44%) aligned 0 times 2758859 (24.71%) aligned exactly 1 time 876404 (7.85%) aligned >1 times 89.79% overall alignment rate Time searching: 00:29:29 Overall time: 00:29:29 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] 18210683 / 30260125 = 0.6018 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 22:46:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.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 22:46:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:46:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:46:18: 1000000 INFO @ Fri, 26 Jun 2020 22:46:24: 2000000 INFO @ Fri, 26 Jun 2020 22:46:30: 3000000 INFO @ Fri, 26 Jun 2020 22:46:35: 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 22:46:41: 5000000 INFO @ Fri, 26 Jun 2020 22:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.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 22:46:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:46:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:46:47: 6000000 INFO @ Fri, 26 Jun 2020 22:46:49: 1000000 INFO @ Fri, 26 Jun 2020 22:46:54: 7000000 INFO @ Fri, 26 Jun 2020 22:46:56: 2000000 INFO @ Fri, 26 Jun 2020 22:47:01: 8000000 INFO @ Fri, 26 Jun 2020 22:47:03: 3000000 INFO @ Fri, 26 Jun 2020 22:47:08: 9000000 INFO @ Fri, 26 Jun 2020 22:47:10: 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 22:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.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 22:47:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:47:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:47:15: 10000000 INFO @ Fri, 26 Jun 2020 22:47:17: 5000000 INFO @ Fri, 26 Jun 2020 22:47:19: 1000000 INFO @ Fri, 26 Jun 2020 22:47:22: 11000000 INFO @ Fri, 26 Jun 2020 22:47:24: 6000000 INFO @ Fri, 26 Jun 2020 22:47:27: 2000000 INFO @ Fri, 26 Jun 2020 22:47:29: 12000000 INFO @ Fri, 26 Jun 2020 22:47:31: 7000000 INFO @ Fri, 26 Jun 2020 22:47:34: 3000000 INFO @ Fri, 26 Jun 2020 22:47:36: 13000000 INFO @ Fri, 26 Jun 2020 22:47:38: 8000000 INFO @ Fri, 26 Jun 2020 22:47:41: 4000000 INFO @ Fri, 26 Jun 2020 22:47:43: 14000000 INFO @ Fri, 26 Jun 2020 22:47:45: 9000000 INFO @ Fri, 26 Jun 2020 22:47:47: 5000000 INFO @ Fri, 26 Jun 2020 22:47:50: 15000000 INFO @ Fri, 26 Jun 2020 22:47:52: 10000000 INFO @ Fri, 26 Jun 2020 22:47:54: 6000000 INFO @ Fri, 26 Jun 2020 22:47:56: 16000000 INFO @ Fri, 26 Jun 2020 22:47:59: 11000000 INFO @ Fri, 26 Jun 2020 22:48:01: 7000000 INFO @ Fri, 26 Jun 2020 22:48:03: 17000000 INFO @ Fri, 26 Jun 2020 22:48:05: 12000000 INFO @ Fri, 26 Jun 2020 22:48:08: 8000000 INFO @ Fri, 26 Jun 2020 22:48:10: 18000000 INFO @ Fri, 26 Jun 2020 22:48:13: 13000000 INFO @ Fri, 26 Jun 2020 22:48:15: 9000000 INFO @ Fri, 26 Jun 2020 22:48:17: 19000000 INFO @ Fri, 26 Jun 2020 22:48:20: 14000000 INFO @ Fri, 26 Jun 2020 22:48:22: 10000000 INFO @ Fri, 26 Jun 2020 22:48:24: 20000000 INFO @ Fri, 26 Jun 2020 22:48:27: 15000000 INFO @ Fri, 26 Jun 2020 22:48:30: 11000000 INFO @ Fri, 26 Jun 2020 22:48:31: 21000000 INFO @ Fri, 26 Jun 2020 22:48:34: 16000000 INFO @ Fri, 26 Jun 2020 22:48:37: 12000000 INFO @ Fri, 26 Jun 2020 22:48:38: 22000000 INFO @ Fri, 26 Jun 2020 22:48:41: 17000000 INFO @ Fri, 26 Jun 2020 22:48:44: 13000000 INFO @ Fri, 26 Jun 2020 22:48:45: 23000000 INFO @ Fri, 26 Jun 2020 22:48:48: 18000000 INFO @ Fri, 26 Jun 2020 22:48:51: 14000000 INFO @ Fri, 26 Jun 2020 22:48:52: 24000000 INFO @ Fri, 26 Jun 2020 22:48:55: 19000000 INFO @ Fri, 26 Jun 2020 22:48:58: 15000000 INFO @ Fri, 26 Jun 2020 22:49:00: 25000000 INFO @ Fri, 26 Jun 2020 22:49:03: 20000000 INFO @ Fri, 26 Jun 2020 22:49:06: 16000000 INFO @ Fri, 26 Jun 2020 22:49:07: 26000000 INFO @ Fri, 26 Jun 2020 22:49:11: 21000000 INFO @ Fri, 26 Jun 2020 22:49:13: 17000000 INFO @ Fri, 26 Jun 2020 22:49:15: 27000000 INFO @ Fri, 26 Jun 2020 22:49:18: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:49:21: 18000000 INFO @ Fri, 26 Jun 2020 22:49:22: 28000000 INFO @ Fri, 26 Jun 2020 22:49:25: 23000000 INFO @ Fri, 26 Jun 2020 22:49:28: 19000000 INFO @ Fri, 26 Jun 2020 22:49:29: 29000000 INFO @ Fri, 26 Jun 2020 22:49:32: 24000000 INFO @ Fri, 26 Jun 2020 22:49:34: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:49:34: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:49:34: #1 total tags in treatment: 11927659 INFO @ Fri, 26 Jun 2020 22:49:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:49:34: #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 22:49:35: #1 tags after filtering in treatment: 10069375 INFO @ Fri, 26 Jun 2020 22:49:35: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 22:49:35: #1 finished! INFO @ Fri, 26 Jun 2020 22:49:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:49:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:49:35: 20000000 INFO @ Fri, 26 Jun 2020 22:49:35: #2 number of paired peaks: 451 WARNING @ Fri, 26 Jun 2020 22:49:35: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 26 Jun 2020 22:49:35: start model_add_line... INFO @ Fri, 26 Jun 2020 22:49:35: start X-correlation... INFO @ Fri, 26 Jun 2020 22:49:35: end of X-cor INFO @ Fri, 26 Jun 2020 22:49:35: #2 finished! INFO @ Fri, 26 Jun 2020 22:49:35: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 22:49:35: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 22:49:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.05_model.r INFO @ Fri, 26 Jun 2020 22:49:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:49:39: 25000000 INFO @ Fri, 26 Jun 2020 22:49:42: 21000000 INFO @ Fri, 26 Jun 2020 22:49:46: 26000000 INFO @ Fri, 26 Jun 2020 22:49:49: 22000000 INFO @ Fri, 26 Jun 2020 22:49:53: 27000000 INFO @ Fri, 26 Jun 2020 22:49:55: 23000000 INFO @ Fri, 26 Jun 2020 22:49:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:49:59: 28000000 INFO @ Fri, 26 Jun 2020 22:50:02: 24000000 INFO @ Fri, 26 Jun 2020 22:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.05_summits.bed INFO @ Fri, 26 Jun 2020 22:50:06: Done! INFO @ Fri, 26 Jun 2020 22:50:06: 29000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2083 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:50:09: 25000000 INFO @ Fri, 26 Jun 2020 22:50:11: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:50:11: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:50:11: #1 total tags in treatment: 11927659 INFO @ Fri, 26 Jun 2020 22:50:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:50:11: #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 22:50:11: #1 tags after filtering in treatment: 10069375 INFO @ Fri, 26 Jun 2020 22:50:11: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 22:50:11: #1 finished! INFO @ Fri, 26 Jun 2020 22:50:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:50:12: #2 number of paired peaks: 451 WARNING @ Fri, 26 Jun 2020 22:50:12: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 26 Jun 2020 22:50:12: start model_add_line... INFO @ Fri, 26 Jun 2020 22:50:12: start X-correlation... INFO @ Fri, 26 Jun 2020 22:50:12: end of X-cor INFO @ Fri, 26 Jun 2020 22:50:12: #2 finished! INFO @ Fri, 26 Jun 2020 22:50:12: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 22:50:12: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 22:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.10_model.r INFO @ Fri, 26 Jun 2020 22:50:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:50:15: 26000000 INFO @ Fri, 26 Jun 2020 22:50:21: 27000000 INFO @ Fri, 26 Jun 2020 22:50:27: 28000000 INFO @ Fri, 26 Jun 2020 22:50:32: 29000000 INFO @ Fri, 26 Jun 2020 22:50:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:50:36: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:50:36: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:50:36: #1 total tags in treatment: 11927659 INFO @ Fri, 26 Jun 2020 22:50:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:50:36: #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 22:50:37: #1 tags after filtering in treatment: 10069375 INFO @ Fri, 26 Jun 2020 22:50:37: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 22:50:37: #1 finished! INFO @ Fri, 26 Jun 2020 22:50:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:50:37: #2 number of paired peaks: 451 WARNING @ Fri, 26 Jun 2020 22:50:37: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 26 Jun 2020 22:50:37: start model_add_line... INFO @ Fri, 26 Jun 2020 22:50:37: start X-correlation... INFO @ Fri, 26 Jun 2020 22:50:37: end of X-cor INFO @ Fri, 26 Jun 2020 22:50:37: #2 finished! INFO @ Fri, 26 Jun 2020 22:50:37: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 22:50:37: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 22:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.20_model.r INFO @ Fri, 26 Jun 2020 22:50:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.10_summits.bed INFO @ Fri, 26 Jun 2020 22:50:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1249 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:50:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:51:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:51:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:51:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085349/SRX4085349.20_summits.bed INFO @ Fri, 26 Jun 2020 22:51:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 2 millis CompletedMACS2peakCalling