Job ID = 6527410 SRX = SRX466528 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:25:48 prefetch.2.10.7: 1) Downloading 'SRR1163594'... 2020-06-29T12:25:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:31:19 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:31:19 prefetch.2.10.7: 1) 'SRR1163594' was downloaded successfully Read 21509609 spots for SRR1163594/SRR1163594.sra Written 21509609 spots for SRR1163594/SRR1163594.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: 00:03:46 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256461 (1.19%) aligned 0 times 17820588 (82.85%) aligned exactly 1 time 3432560 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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 8 files... [bam_rmdupse_core] 3667983 / 21253148 = 0.1726 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 @ Mon, 29 Jun 2020 21:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.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 @ Mon, 29 Jun 2020 21:47:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:47:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:48:02: 1000000 INFO @ Mon, 29 Jun 2020 21:48:07: 2000000 INFO @ Mon, 29 Jun 2020 21:48:11: 3000000 INFO @ Mon, 29 Jun 2020 21:48:16: 4000000 INFO @ Mon, 29 Jun 2020 21:48:21: 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 @ Mon, 29 Jun 2020 21:48:26: 6000000 INFO @ Mon, 29 Jun 2020 21:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.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 @ Mon, 29 Jun 2020 21:48:27: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:48:27: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:48:31: 7000000 INFO @ Mon, 29 Jun 2020 21:48:32: 1000000 INFO @ Mon, 29 Jun 2020 21:48:36: 8000000 INFO @ Mon, 29 Jun 2020 21:48:38: 2000000 INFO @ Mon, 29 Jun 2020 21:48:41: 9000000 INFO @ Mon, 29 Jun 2020 21:48:43: 3000000 INFO @ Mon, 29 Jun 2020 21:48:46: 10000000 INFO @ Mon, 29 Jun 2020 21:48:48: 4000000 INFO @ Mon, 29 Jun 2020 21:48:51: 11000000 INFO @ Mon, 29 Jun 2020 21:48:53: 5000000 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 @ Mon, 29 Jun 2020 21:48:57: 12000000 INFO @ Mon, 29 Jun 2020 21:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.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 @ Mon, 29 Jun 2020 21:48:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:48:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:48:58: 6000000 INFO @ Mon, 29 Jun 2020 21:49:02: 13000000 INFO @ Mon, 29 Jun 2020 21:49:03: 1000000 INFO @ Mon, 29 Jun 2020 21:49:03: 7000000 INFO @ Mon, 29 Jun 2020 21:49:07: 14000000 INFO @ Mon, 29 Jun 2020 21:49:08: 2000000 INFO @ Mon, 29 Jun 2020 21:49:08: 8000000 INFO @ Mon, 29 Jun 2020 21:49:12: 15000000 INFO @ Mon, 29 Jun 2020 21:49:13: 9000000 INFO @ Mon, 29 Jun 2020 21:49:13: 3000000 INFO @ Mon, 29 Jun 2020 21:49:17: 16000000 INFO @ Mon, 29 Jun 2020 21:49:18: 10000000 INFO @ Mon, 29 Jun 2020 21:49:19: 4000000 INFO @ Mon, 29 Jun 2020 21:49:22: 17000000 INFO @ Mon, 29 Jun 2020 21:49:23: 11000000 INFO @ Mon, 29 Jun 2020 21:49:24: 5000000 INFO @ Mon, 29 Jun 2020 21:49:25: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:49:25: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:49:25: #1 total tags in treatment: 17585165 INFO @ Mon, 29 Jun 2020 21:49:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:49:26: #1 tags after filtering in treatment: 17585165 INFO @ Mon, 29 Jun 2020 21:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:26: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:27: #2 number of paired peaks: 200 WARNING @ Mon, 29 Jun 2020 21:49:27: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:27: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:27: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:27: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:27: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:27: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 21:49:27: #2 alternative fragment length(s) may be 1,38,585 bps INFO @ Mon, 29 Jun 2020 21:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.05_model.r WARNING @ Mon, 29 Jun 2020 21:49:27: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:27: #2 You may need to consider one of the other alternative d(s): 1,38,585 WARNING @ Mon, 29 Jun 2020 21:49:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:49:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:49:28: 12000000 INFO @ Mon, 29 Jun 2020 21:49:30: 6000000 INFO @ Mon, 29 Jun 2020 21:49:33: 13000000 INFO @ Mon, 29 Jun 2020 21:49:35: 7000000 INFO @ Mon, 29 Jun 2020 21:49:37: 14000000 INFO @ Mon, 29 Jun 2020 21:49:40: 8000000 INFO @ Mon, 29 Jun 2020 21:49:42: 15000000 INFO @ Mon, 29 Jun 2020 21:49:45: 9000000 INFO @ Mon, 29 Jun 2020 21:49:47: 16000000 INFO @ Mon, 29 Jun 2020 21:49:50: 10000000 INFO @ Mon, 29 Jun 2020 21:49:52: 17000000 INFO @ Mon, 29 Jun 2020 21:49:55: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:49:55: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:49:55: #1 total tags in treatment: 17585165 INFO @ Mon, 29 Jun 2020 21:49:55: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:49:55: #1 tags after filtering in treatment: 17585165 INFO @ Mon, 29 Jun 2020 21:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:55: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:55: 11000000 INFO @ Mon, 29 Jun 2020 21:49:56: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:49:56: #2 number of paired peaks: 200 WARNING @ Mon, 29 Jun 2020 21:49:56: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:56: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:56: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:56: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:56: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:56: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 21:49:56: #2 alternative fragment length(s) may be 1,38,585 bps INFO @ Mon, 29 Jun 2020 21:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.10_model.r WARNING @ Mon, 29 Jun 2020 21:49:56: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:56: #2 You may need to consider one of the other alternative d(s): 1,38,585 WARNING @ Mon, 29 Jun 2020 21:49:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:49:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:50:00: 12000000 INFO @ Mon, 29 Jun 2020 21:50:05: 13000000 INFO @ Mon, 29 Jun 2020 21:50:10: 14000000 INFO @ Mon, 29 Jun 2020 21:50:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.05_summits.bed INFO @ Mon, 29 Jun 2020 21:50:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (697 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:50:15: 15000000 INFO @ Mon, 29 Jun 2020 21:50:20: 16000000 INFO @ Mon, 29 Jun 2020 21:50:24: 17000000 INFO @ Mon, 29 Jun 2020 21:50:24: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:50:27: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:50:27: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:50:27: #1 total tags in treatment: 17585165 INFO @ Mon, 29 Jun 2020 21:50:27: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:50:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:50:28: #1 tags after filtering in treatment: 17585165 INFO @ Mon, 29 Jun 2020 21:50:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:50:28: #1 finished! INFO @ Mon, 29 Jun 2020 21:50:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:50:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:50:29: #2 number of paired peaks: 200 WARNING @ Mon, 29 Jun 2020 21:50:29: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 29 Jun 2020 21:50:29: start model_add_line... INFO @ Mon, 29 Jun 2020 21:50:29: start X-correlation... INFO @ Mon, 29 Jun 2020 21:50:29: end of X-cor INFO @ Mon, 29 Jun 2020 21:50:29: #2 finished! INFO @ Mon, 29 Jun 2020 21:50:29: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 21:50:29: #2 alternative fragment length(s) may be 1,38,585 bps INFO @ Mon, 29 Jun 2020 21:50:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.20_model.r WARNING @ Mon, 29 Jun 2020 21:50:29: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:50:29: #2 You may need to consider one of the other alternative d(s): 1,38,585 WARNING @ Mon, 29 Jun 2020 21:50:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:50:29: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:50:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.10_summits.bed INFO @ Mon, 29 Jun 2020 21:50:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (334 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:50:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:51:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:51:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466528/SRX466528.20_summits.bed INFO @ Mon, 29 Jun 2020 21:51:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。