Job ID = 6507743 SRX = SRX2011721 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T12:53:56 prefetch.2.10.7: 1) Downloading 'SRR4017963'... 2020-06-26T12:53:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:58:44 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:58:44 prefetch.2.10.7: 1) 'SRR4017963' was downloaded successfully Read 15974307 spots for SRR4017963/SRR4017963.sra Written 15974307 spots for SRR4017963/SRR4017963.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: 00:25:09 15974307 reads; of these: 15974307 (100.00%) were paired; of these: 1694355 (10.61%) aligned concordantly 0 times 12342880 (77.27%) aligned concordantly exactly 1 time 1937072 (12.13%) aligned concordantly >1 times ---- 1694355 pairs aligned concordantly 0 times; of these: 1235427 (72.91%) aligned discordantly 1 time ---- 458928 pairs aligned 0 times concordantly or discordantly; of these: 917856 mates make up the pairs; of these: 318435 (34.69%) aligned 0 times 275655 (30.03%) aligned exactly 1 time 323766 (35.27%) aligned >1 times 99.00% overall alignment rate Time searching: 00:25:09 Overall time: 00:25:09 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] 1955724 / 15357154 = 0.1273 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 22:40:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.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 22:40:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:40:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:40:22: 1000000 INFO @ Fri, 26 Jun 2020 22:40:31: 2000000 INFO @ Fri, 26 Jun 2020 22:40:39: 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 22:40:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.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 22:40:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:40:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:40:47: 4000000 INFO @ Fri, 26 Jun 2020 22:40:54: 1000000 INFO @ Fri, 26 Jun 2020 22:40:56: 5000000 INFO @ Fri, 26 Jun 2020 22:41:04: 2000000 INFO @ Fri, 26 Jun 2020 22:41:06: 6000000 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 22:41:13: 3000000 INFO @ Fri, 26 Jun 2020 22:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.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 22:41:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:41:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:41:15: 7000000 INFO @ Fri, 26 Jun 2020 22:41:23: 4000000 INFO @ Fri, 26 Jun 2020 22:41:24: 1000000 INFO @ Fri, 26 Jun 2020 22:41:24: 8000000 INFO @ Fri, 26 Jun 2020 22:41:32: 5000000 INFO @ Fri, 26 Jun 2020 22:41:34: 2000000 INFO @ Fri, 26 Jun 2020 22:41:34: 9000000 INFO @ Fri, 26 Jun 2020 22:41:42: 6000000 INFO @ Fri, 26 Jun 2020 22:41:43: 3000000 INFO @ Fri, 26 Jun 2020 22:41:44: 10000000 INFO @ Fri, 26 Jun 2020 22:41:52: 7000000 INFO @ Fri, 26 Jun 2020 22:41:53: 4000000 INFO @ Fri, 26 Jun 2020 22:41:53: 11000000 INFO @ Fri, 26 Jun 2020 22:42:01: 8000000 INFO @ Fri, 26 Jun 2020 22:42:03: 5000000 INFO @ Fri, 26 Jun 2020 22:42:03: 12000000 INFO @ Fri, 26 Jun 2020 22:42:11: 9000000 INFO @ Fri, 26 Jun 2020 22:42:13: 6000000 INFO @ Fri, 26 Jun 2020 22:42:13: 13000000 INFO @ Fri, 26 Jun 2020 22:42:21: 10000000 INFO @ Fri, 26 Jun 2020 22:42:23: 7000000 INFO @ Fri, 26 Jun 2020 22:42:23: 14000000 INFO @ Fri, 26 Jun 2020 22:42:31: 11000000 INFO @ Fri, 26 Jun 2020 22:42:32: 8000000 INFO @ Fri, 26 Jun 2020 22:42:33: 15000000 INFO @ Fri, 26 Jun 2020 22:42:41: 12000000 INFO @ Fri, 26 Jun 2020 22:42:42: 9000000 INFO @ Fri, 26 Jun 2020 22:42:43: 16000000 INFO @ Fri, 26 Jun 2020 22:42:51: 13000000 INFO @ Fri, 26 Jun 2020 22:42:52: 10000000 INFO @ Fri, 26 Jun 2020 22:42:53: 17000000 INFO @ Fri, 26 Jun 2020 22:43:01: 14000000 INFO @ Fri, 26 Jun 2020 22:43:02: 11000000 INFO @ Fri, 26 Jun 2020 22:43:03: 18000000 INFO @ Fri, 26 Jun 2020 22:43:11: 15000000 INFO @ Fri, 26 Jun 2020 22:43:12: 12000000 INFO @ Fri, 26 Jun 2020 22:43:13: 19000000 INFO @ Fri, 26 Jun 2020 22:43:21: 16000000 INFO @ Fri, 26 Jun 2020 22:43:22: 13000000 INFO @ Fri, 26 Jun 2020 22:43:22: 20000000 INFO @ Fri, 26 Jun 2020 22:43:31: 17000000 INFO @ Fri, 26 Jun 2020 22:43:32: 14000000 INFO @ Fri, 26 Jun 2020 22:43:32: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:43:41: 18000000 INFO @ Fri, 26 Jun 2020 22:43:41: 15000000 INFO @ Fri, 26 Jun 2020 22:43:42: 22000000 INFO @ Fri, 26 Jun 2020 22:43:51: 16000000 INFO @ Fri, 26 Jun 2020 22:43:51: 19000000 INFO @ Fri, 26 Jun 2020 22:43:52: 23000000 INFO @ Fri, 26 Jun 2020 22:44:01: 17000000 INFO @ Fri, 26 Jun 2020 22:44:01: 20000000 INFO @ Fri, 26 Jun 2020 22:44:01: 24000000 INFO @ Fri, 26 Jun 2020 22:44:11: 18000000 INFO @ Fri, 26 Jun 2020 22:44:11: 21000000 INFO @ Fri, 26 Jun 2020 22:44:11: 25000000 INFO @ Fri, 26 Jun 2020 22:44:21: 19000000 INFO @ Fri, 26 Jun 2020 22:44:21: 22000000 INFO @ Fri, 26 Jun 2020 22:44:22: 26000000 INFO @ Fri, 26 Jun 2020 22:44:31: 20000000 INFO @ Fri, 26 Jun 2020 22:44:31: 27000000 INFO @ Fri, 26 Jun 2020 22:44:32: 23000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:44:38: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 22:44:38: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 22:44:38: #1 total tags in treatment: 12378569 INFO @ Fri, 26 Jun 2020 22:44:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:44:38: #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 22:44:39: #1 tags after filtering in treatment: 11203783 INFO @ Fri, 26 Jun 2020 22:44:39: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:44:39: #1 finished! INFO @ Fri, 26 Jun 2020 22:44:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:44:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:44:39: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:44:39: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:44:39: start model_add_line... INFO @ Fri, 26 Jun 2020 22:44:39: start X-correlation... INFO @ Fri, 26 Jun 2020 22:44:39: end of X-cor INFO @ Fri, 26 Jun 2020 22:44:39: #2 finished! INFO @ Fri, 26 Jun 2020 22:44:39: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 22:44:39: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 22:44:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.05_model.r WARNING @ Fri, 26 Jun 2020 22:44:40: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:44:40: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 22:44:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:44:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:44:40: 21000000 INFO @ Fri, 26 Jun 2020 22:44:42: 24000000 INFO @ Fri, 26 Jun 2020 22:44:50: 22000000 INFO @ Fri, 26 Jun 2020 22:44:52: 25000000 INFO @ Fri, 26 Jun 2020 22:44:59: 23000000 INFO @ Fri, 26 Jun 2020 22:45:02: 26000000 INFO @ Fri, 26 Jun 2020 22:45:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:45:09: 24000000 INFO @ Fri, 26 Jun 2020 22:45:12: 27000000 INFO @ Fri, 26 Jun 2020 22:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:45:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.05_summits.bed INFO @ Fri, 26 Jun 2020 22:45:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (393 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:45:18: 25000000 INFO @ Fri, 26 Jun 2020 22:45:19: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 22:45:19: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 22:45:19: #1 total tags in treatment: 12378569 INFO @ Fri, 26 Jun 2020 22:45:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:45:19: #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 22:45:20: #1 tags after filtering in treatment: 11203783 INFO @ Fri, 26 Jun 2020 22:45:20: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:45:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:45:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:45:20: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:45:20: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:45:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:45:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:45:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:45:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:45:20: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 22:45:20: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 22:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.10_model.r WARNING @ Fri, 26 Jun 2020 22:45:20: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:45:20: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 22:45:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:45:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:45:27: 26000000 INFO @ Fri, 26 Jun 2020 22:45:35: 27000000 INFO @ Fri, 26 Jun 2020 22:45:40: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 22:45:40: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 22:45:40: #1 total tags in treatment: 12378569 INFO @ Fri, 26 Jun 2020 22:45:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:45:40: #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 22:45:40: #1 tags after filtering in treatment: 11203783 INFO @ Fri, 26 Jun 2020 22:45:40: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:45:40: #1 finished! INFO @ Fri, 26 Jun 2020 22:45:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:45:41: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:45:41: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:45:41: start model_add_line... INFO @ Fri, 26 Jun 2020 22:45:41: start X-correlation... INFO @ Fri, 26 Jun 2020 22:45:41: end of X-cor INFO @ Fri, 26 Jun 2020 22:45:41: #2 finished! INFO @ Fri, 26 Jun 2020 22:45:41: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 22:45:41: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 22:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.20_model.r WARNING @ Fri, 26 Jun 2020 22:45:41: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:45:41: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 22:45:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:45:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:45:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.10_summits.bed INFO @ Fri, 26 Jun 2020 22:45:57: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (300 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:46:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011721/SRX2011721.20_summits.bed INFO @ Fri, 26 Jun 2020 22:46:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 1 millis CompletedMACS2peakCalling