Job ID = 6367863 SRX = SRX4085430 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 'SRR7167459'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:04 prefetch.2.10.7: 1) 'SRR7167459' was downloaded successfully Read 16787610 spots for SRR7167459/SRR7167459.sra Written 16787610 spots for SRR7167459/SRR7167459.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: 00:14:41 16787610 reads; of these: 16787610 (100.00%) were paired; of these: 919922 (5.48%) aligned concordantly 0 times 13816127 (82.30%) aligned concordantly exactly 1 time 2051561 (12.22%) aligned concordantly >1 times ---- 919922 pairs aligned concordantly 0 times; of these: 97781 (10.63%) aligned discordantly 1 time ---- 822141 pairs aligned 0 times concordantly or discordantly; of these: 1644282 mates make up the pairs; of these: 1109488 (67.48%) aligned 0 times 416719 (25.34%) aligned exactly 1 time 118075 (7.18%) aligned >1 times 96.70% 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] 1739345 / 15936123 = 0.1091 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 09:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.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 09:14:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:38: 1000000 INFO @ Tue, 16 Jun 2020 09:14:43: 2000000 INFO @ Tue, 16 Jun 2020 09:14:48: 3000000 INFO @ Tue, 16 Jun 2020 09:14:52: 4000000 INFO @ Tue, 16 Jun 2020 09:14:57: 5000000 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 09:15:02: 6000000 INFO @ Tue, 16 Jun 2020 09:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.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 09:15:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:06: 7000000 INFO @ Tue, 16 Jun 2020 09:15:08: 1000000 INFO @ Tue, 16 Jun 2020 09:15:11: 8000000 INFO @ Tue, 16 Jun 2020 09:15:13: 2000000 INFO @ Tue, 16 Jun 2020 09:15:16: 9000000 INFO @ Tue, 16 Jun 2020 09:15:18: 3000000 INFO @ Tue, 16 Jun 2020 09:15:21: 10000000 INFO @ Tue, 16 Jun 2020 09:15:23: 4000000 INFO @ Tue, 16 Jun 2020 09:15:26: 11000000 INFO @ Tue, 16 Jun 2020 09:15:27: 5000000 INFO @ Tue, 16 Jun 2020 09:15:30: 12000000 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 09:15:32: 6000000 INFO @ Tue, 16 Jun 2020 09:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.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 09:15:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:35: 13000000 INFO @ Tue, 16 Jun 2020 09:15:37: 7000000 INFO @ Tue, 16 Jun 2020 09:15:39: 1000000 INFO @ Tue, 16 Jun 2020 09:15:40: 14000000 INFO @ Tue, 16 Jun 2020 09:15:42: 8000000 INFO @ Tue, 16 Jun 2020 09:15:44: 2000000 INFO @ Tue, 16 Jun 2020 09:15:45: 15000000 INFO @ Tue, 16 Jun 2020 09:15:46: 9000000 INFO @ Tue, 16 Jun 2020 09:15:49: 3000000 INFO @ Tue, 16 Jun 2020 09:15:49: 16000000 INFO @ Tue, 16 Jun 2020 09:15:51: 10000000 INFO @ Tue, 16 Jun 2020 09:15:54: 17000000 INFO @ Tue, 16 Jun 2020 09:15:54: 4000000 INFO @ Tue, 16 Jun 2020 09:15:56: 11000000 INFO @ Tue, 16 Jun 2020 09:15:59: 18000000 INFO @ Tue, 16 Jun 2020 09:15:59: 5000000 INFO @ Tue, 16 Jun 2020 09:16:01: 12000000 INFO @ Tue, 16 Jun 2020 09:16:04: 19000000 INFO @ Tue, 16 Jun 2020 09:16:05: 6000000 INFO @ Tue, 16 Jun 2020 09:16:05: 13000000 INFO @ Tue, 16 Jun 2020 09:16:08: 20000000 INFO @ Tue, 16 Jun 2020 09:16:10: 7000000 INFO @ Tue, 16 Jun 2020 09:16:10: 14000000 INFO @ Tue, 16 Jun 2020 09:16:13: 21000000 INFO @ Tue, 16 Jun 2020 09:16:14: 8000000 INFO @ Tue, 16 Jun 2020 09:16:15: 15000000 INFO @ Tue, 16 Jun 2020 09:16:18: 22000000 INFO @ Tue, 16 Jun 2020 09:16:19: 9000000 INFO @ Tue, 16 Jun 2020 09:16:20: 16000000 INFO @ Tue, 16 Jun 2020 09:16:22: 23000000 INFO @ Tue, 16 Jun 2020 09:16:24: 10000000 INFO @ Tue, 16 Jun 2020 09:16:24: 17000000 INFO @ Tue, 16 Jun 2020 09:16:27: 24000000 INFO @ Tue, 16 Jun 2020 09:16:29: 11000000 INFO @ Tue, 16 Jun 2020 09:16:29: 18000000 INFO @ Tue, 16 Jun 2020 09:16:32: 25000000 INFO @ Tue, 16 Jun 2020 09:16:34: 12000000 INFO @ Tue, 16 Jun 2020 09:16:34: 19000000 INFO @ Tue, 16 Jun 2020 09:16:37: 26000000 INFO @ Tue, 16 Jun 2020 09:16:39: 13000000 INFO @ Tue, 16 Jun 2020 09:16:39: 20000000 INFO @ Tue, 16 Jun 2020 09:16:42: 27000000 INFO @ Tue, 16 Jun 2020 09:16:44: 14000000 INFO @ Tue, 16 Jun 2020 09:16:44: 21000000 INFO @ Tue, 16 Jun 2020 09:16:46: 28000000 INFO @ Tue, 16 Jun 2020 09:16:48: 15000000 INFO @ Tue, 16 Jun 2020 09:16:49: 22000000 INFO @ Tue, 16 Jun 2020 09:16:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:51: #1 total tags in treatment: 14132462 INFO @ Tue, 16 Jun 2020 09:16:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:51: #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 09:16:51: #1 tags after filtering in treatment: 11946564 INFO @ Tue, 16 Jun 2020 09:16:51: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:16:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:52: #2 number of paired peaks: 181 WARNING @ Tue, 16 Jun 2020 09:16:52: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:52: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:16:52: #2 alternative fragment length(s) may be 2,107,124,160 bps INFO @ Tue, 16 Jun 2020 09:16:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.05_model.r INFO @ Tue, 16 Jun 2020 09:16:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:53: 16000000 INFO @ Tue, 16 Jun 2020 09:16:53: 23000000 INFO @ Tue, 16 Jun 2020 09:16:58: 17000000 INFO @ Tue, 16 Jun 2020 09:16:58: 24000000 INFO @ Tue, 16 Jun 2020 09:17:03: 18000000 INFO @ Tue, 16 Jun 2020 09:17:03: 25000000 INFO @ Tue, 16 Jun 2020 09:17:08: 19000000 INFO @ Tue, 16 Jun 2020 09:17:08: 26000000 INFO @ Tue, 16 Jun 2020 09:17:12: 27000000 INFO @ Tue, 16 Jun 2020 09:17:12: 20000000 INFO @ Tue, 16 Jun 2020 09:17:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:17: 28000000 INFO @ Tue, 16 Jun 2020 09:17:17: 21000000 INFO @ Tue, 16 Jun 2020 09:17:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:22: #1 total tags in treatment: 14132462 INFO @ Tue, 16 Jun 2020 09:17:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:22: #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 09:17:22: 22000000 INFO @ Tue, 16 Jun 2020 09:17:22: #1 tags after filtering in treatment: 11946564 INFO @ Tue, 16 Jun 2020 09:17:22: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:17:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:23: #2 number of paired peaks: 181 WARNING @ Tue, 16 Jun 2020 09:17:23: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:23: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:17:23: #2 alternative fragment length(s) may be 2,107,124,160 bps INFO @ Tue, 16 Jun 2020 09:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.10_model.r INFO @ Tue, 16 Jun 2020 09:17:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:27: 23000000 INFO @ Tue, 16 Jun 2020 09:17:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1311 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:32: 24000000 INFO @ Tue, 16 Jun 2020 09:17:36: 25000000 INFO @ Tue, 16 Jun 2020 09:17:41: 26000000 INFO @ Tue, 16 Jun 2020 09:17:46: 27000000 INFO @ Tue, 16 Jun 2020 09:17:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:51: 28000000 INFO @ Tue, 16 Jun 2020 09:17:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:56: #1 total tags in treatment: 14132462 INFO @ Tue, 16 Jun 2020 09:17:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:56: #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 09:17:56: #1 tags after filtering in treatment: 11946564 INFO @ Tue, 16 Jun 2020 09:17:56: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:17:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:57: #2 number of paired peaks: 181 WARNING @ Tue, 16 Jun 2020 09:17:57: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:57: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:17:57: #2 alternative fragment length(s) may be 2,107,124,160 bps INFO @ Tue, 16 Jun 2020 09:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.20_model.r INFO @ Tue, 16 Jun 2020 09:17:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.10_summits.bed INFO @ Tue, 16 Jun 2020 09:18:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:18:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085430/SRX4085430.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (137 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。