Job ID = 6497383 SRX = SRX4085363 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:58:57 prefetch.2.10.7: 1) Downloading 'SRR7167392'... 2020-06-25T21:58:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:02:33 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:02:33 prefetch.2.10.7: 1) 'SRR7167392' was downloaded successfully Read 13503380 spots for SRR7167392/SRR7167392.sra Written 13503380 spots for SRR7167392/SRR7167392.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: 00:10:49 13503380 reads; of these: 13503380 (100.00%) were paired; of these: 526799 (3.90%) aligned concordantly 0 times 11496505 (85.14%) aligned concordantly exactly 1 time 1480076 (10.96%) aligned concordantly >1 times ---- 526799 pairs aligned concordantly 0 times; of these: 91922 (17.45%) aligned discordantly 1 time ---- 434877 pairs aligned 0 times concordantly or discordantly; of these: 869754 mates make up the pairs; of these: 468716 (53.89%) aligned 0 times 316041 (36.34%) aligned exactly 1 time 84997 (9.77%) aligned >1 times 98.26% overall alignment rate Time searching: 00:10:49 Overall time: 00:10:49 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 12 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] 1441082 / 13018397 = 0.1107 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 07:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.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 07:22:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:30: 1000000 INFO @ Fri, 26 Jun 2020 07:22:37: 2000000 INFO @ Fri, 26 Jun 2020 07:22:44: 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 @ Fri, 26 Jun 2020 07:22:51: 4000000 INFO @ Fri, 26 Jun 2020 07:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.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 07:22:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:59: 5000000 INFO @ Fri, 26 Jun 2020 07:23:00: 1000000 INFO @ Fri, 26 Jun 2020 07:23:07: 6000000 INFO @ Fri, 26 Jun 2020 07:23:08: 2000000 INFO @ Fri, 26 Jun 2020 07:23:15: 7000000 INFO @ Fri, 26 Jun 2020 07:23:16: 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 @ Fri, 26 Jun 2020 07:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.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 07:23:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:23:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:23:24: 4000000 INFO @ Fri, 26 Jun 2020 07:23:24: 8000000 INFO @ Fri, 26 Jun 2020 07:23:30: 1000000 INFO @ Fri, 26 Jun 2020 07:23:32: 5000000 INFO @ Fri, 26 Jun 2020 07:23:32: 9000000 INFO @ Fri, 26 Jun 2020 07:23:37: 2000000 INFO @ Fri, 26 Jun 2020 07:23:40: 6000000 INFO @ Fri, 26 Jun 2020 07:23:41: 10000000 INFO @ Fri, 26 Jun 2020 07:23:45: 3000000 INFO @ Fri, 26 Jun 2020 07:23:48: 7000000 INFO @ Fri, 26 Jun 2020 07:23:49: 11000000 INFO @ Fri, 26 Jun 2020 07:23:53: 4000000 INFO @ Fri, 26 Jun 2020 07:23:56: 8000000 INFO @ Fri, 26 Jun 2020 07:23:57: 12000000 INFO @ Fri, 26 Jun 2020 07:24:00: 5000000 INFO @ Fri, 26 Jun 2020 07:24:04: 9000000 INFO @ Fri, 26 Jun 2020 07:24:05: 13000000 INFO @ Fri, 26 Jun 2020 07:24:08: 6000000 INFO @ Fri, 26 Jun 2020 07:24:12: 10000000 INFO @ Fri, 26 Jun 2020 07:24:13: 14000000 INFO @ Fri, 26 Jun 2020 07:24:15: 7000000 INFO @ Fri, 26 Jun 2020 07:24:20: 11000000 INFO @ Fri, 26 Jun 2020 07:24:22: 15000000 INFO @ Fri, 26 Jun 2020 07:24:22: 8000000 INFO @ Fri, 26 Jun 2020 07:24:29: 12000000 INFO @ Fri, 26 Jun 2020 07:24:30: 16000000 INFO @ Fri, 26 Jun 2020 07:24:30: 9000000 INFO @ Fri, 26 Jun 2020 07:24:37: 13000000 INFO @ Fri, 26 Jun 2020 07:24:37: 10000000 INFO @ Fri, 26 Jun 2020 07:24:38: 17000000 INFO @ Fri, 26 Jun 2020 07:24:44: 11000000 INFO @ Fri, 26 Jun 2020 07:24:45: 14000000 INFO @ Fri, 26 Jun 2020 07:24:46: 18000000 INFO @ Fri, 26 Jun 2020 07:24:52: 12000000 INFO @ Fri, 26 Jun 2020 07:24:53: 15000000 INFO @ Fri, 26 Jun 2020 07:24:54: 19000000 INFO @ Fri, 26 Jun 2020 07:24:59: 13000000 INFO @ Fri, 26 Jun 2020 07:25:01: 16000000 INFO @ Fri, 26 Jun 2020 07:25:02: 20000000 INFO @ Fri, 26 Jun 2020 07:25:07: 14000000 INFO @ Fri, 26 Jun 2020 07:25:09: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:25:10: 21000000 INFO @ Fri, 26 Jun 2020 07:25:14: 15000000 INFO @ Fri, 26 Jun 2020 07:25:17: 18000000 INFO @ Fri, 26 Jun 2020 07:25:18: 22000000 INFO @ Fri, 26 Jun 2020 07:25:22: 16000000 INFO @ Fri, 26 Jun 2020 07:25:25: 19000000 INFO @ Fri, 26 Jun 2020 07:25:26: 23000000 INFO @ Fri, 26 Jun 2020 07:25:30: 17000000 INFO @ Fri, 26 Jun 2020 07:25:32: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:25:32: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:25:32: #1 total tags in treatment: 11538477 INFO @ Fri, 26 Jun 2020 07:25:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:25:32: #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 07:25:32: #1 tags after filtering in treatment: 10414504 INFO @ Fri, 26 Jun 2020 07:25:32: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 07:25:32: #1 finished! INFO @ Fri, 26 Jun 2020 07:25:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:25:33: #2 number of paired peaks: 168 WARNING @ Fri, 26 Jun 2020 07:25:33: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 26 Jun 2020 07:25:33: start model_add_line... INFO @ Fri, 26 Jun 2020 07:25:33: start X-correlation... INFO @ Fri, 26 Jun 2020 07:25:33: end of X-cor INFO @ Fri, 26 Jun 2020 07:25:33: #2 finished! INFO @ Fri, 26 Jun 2020 07:25:33: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 07:25:33: #2 alternative fragment length(s) may be 4,124,145,172 bps INFO @ Fri, 26 Jun 2020 07:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.05_model.r INFO @ Fri, 26 Jun 2020 07:25:34: 20000000 INFO @ Fri, 26 Jun 2020 07:25:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:25:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:25:37: 18000000 INFO @ Fri, 26 Jun 2020 07:25:43: 21000000 INFO @ Fri, 26 Jun 2020 07:25:45: 19000000 INFO @ Fri, 26 Jun 2020 07:25:51: 22000000 INFO @ Fri, 26 Jun 2020 07:25:52: 20000000 INFO @ Fri, 26 Jun 2020 07:25:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:25:59: 23000000 INFO @ Fri, 26 Jun 2020 07:26:00: 21000000 INFO @ Fri, 26 Jun 2020 07:26:04: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:26:04: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:26:04: #1 total tags in treatment: 11538477 INFO @ Fri, 26 Jun 2020 07:26:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:26:04: #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 07:26:04: #1 tags after filtering in treatment: 10414504 INFO @ Fri, 26 Jun 2020 07:26:04: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 07:26:04: #1 finished! INFO @ Fri, 26 Jun 2020 07:26:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:26:05: #2 number of paired peaks: 168 WARNING @ Fri, 26 Jun 2020 07:26:05: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 26 Jun 2020 07:26:05: start model_add_line... INFO @ Fri, 26 Jun 2020 07:26:05: start X-correlation... INFO @ Fri, 26 Jun 2020 07:26:05: end of X-cor INFO @ Fri, 26 Jun 2020 07:26:05: #2 finished! INFO @ Fri, 26 Jun 2020 07:26:05: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 07:26:05: #2 alternative fragment length(s) may be 4,124,145,172 bps INFO @ Fri, 26 Jun 2020 07:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.10_model.r INFO @ Fri, 26 Jun 2020 07:26:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:26:07: 22000000 INFO @ Fri, 26 Jun 2020 07:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:26:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:26:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.05_summits.bed INFO @ Fri, 26 Jun 2020 07:26:10: Done! INFO @ Fri, 26 Jun 2020 07:26:14: 23000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:26:18: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:26:18: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:26:18: #1 total tags in treatment: 11538477 INFO @ Fri, 26 Jun 2020 07:26:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:26:18: #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 07:26:18: #1 tags after filtering in treatment: 10414504 INFO @ Fri, 26 Jun 2020 07:26:18: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 07:26:18: #1 finished! INFO @ Fri, 26 Jun 2020 07:26:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:26:19: #2 number of paired peaks: 168 WARNING @ Fri, 26 Jun 2020 07:26:19: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 26 Jun 2020 07:26:19: start model_add_line... INFO @ Fri, 26 Jun 2020 07:26:19: start X-correlation... INFO @ Fri, 26 Jun 2020 07:26:19: end of X-cor INFO @ Fri, 26 Jun 2020 07:26:19: #2 finished! INFO @ Fri, 26 Jun 2020 07:26:19: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 07:26:19: #2 alternative fragment length(s) may be 4,124,145,172 bps INFO @ Fri, 26 Jun 2020 07:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.20_model.r INFO @ Fri, 26 Jun 2020 07:26:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:26:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:26:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:26:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:26:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.10_summits.bed INFO @ Fri, 26 Jun 2020 07:26:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (170 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:26:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085363/SRX4085363.20_summits.bed INFO @ Fri, 26 Jun 2020 07:26:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 1 millis CompletedMACS2peakCalling