Job ID = 6527411 SRX = SRX466543 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:19:56 prefetch.2.10.7: 1) Downloading 'SRR1163609'... 2020-06-29T12:19:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:25:00 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:25:00 prefetch.2.10.7: 1) 'SRR1163609' was downloaded successfully Read 21509609 spots for SRR1163609/SRR1163609.sra Written 21509609 spots for SRR1163609/SRR1163609.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: 00:04:03 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256438 (1.19%) aligned 0 times 17820582 (82.85%) aligned exactly 1 time 3432589 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 3667645 / 21253171 = 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 21:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.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 21:39:25: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:39:25: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:39:30: 1000000 INFO @ Mon, 29 Jun 2020 21:39:35: 2000000 INFO @ Mon, 29 Jun 2020 21:39:40: 3000000 INFO @ Mon, 29 Jun 2020 21:39:45: 4000000 INFO @ Mon, 29 Jun 2020 21:39:50: 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 21:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.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 21:39:54: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:39:54: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:39:56: 6000000 INFO @ Mon, 29 Jun 2020 21:39:59: 1000000 INFO @ Mon, 29 Jun 2020 21:40:01: 7000000 INFO @ Mon, 29 Jun 2020 21:40:04: 2000000 INFO @ Mon, 29 Jun 2020 21:40:06: 8000000 INFO @ Mon, 29 Jun 2020 21:40:08: 3000000 INFO @ Mon, 29 Jun 2020 21:40:11: 9000000 INFO @ Mon, 29 Jun 2020 21:40:13: 4000000 INFO @ Mon, 29 Jun 2020 21:40:16: 10000000 INFO @ Mon, 29 Jun 2020 21:40:18: 5000000 INFO @ Mon, 29 Jun 2020 21:40:21: 11000000 INFO @ Mon, 29 Jun 2020 21:40:22: 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 @ Mon, 29 Jun 2020 21:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.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 21:40:25: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:40:25: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:40:27: 12000000 INFO @ Mon, 29 Jun 2020 21:40:27: 7000000 INFO @ Mon, 29 Jun 2020 21:40:29: 1000000 INFO @ Mon, 29 Jun 2020 21:40:32: 8000000 INFO @ Mon, 29 Jun 2020 21:40:32: 13000000 INFO @ Mon, 29 Jun 2020 21:40:34: 2000000 INFO @ Mon, 29 Jun 2020 21:40:36: 9000000 INFO @ Mon, 29 Jun 2020 21:40:37: 14000000 INFO @ Mon, 29 Jun 2020 21:40:39: 3000000 INFO @ Mon, 29 Jun 2020 21:40:41: 10000000 INFO @ Mon, 29 Jun 2020 21:40:42: 15000000 INFO @ Mon, 29 Jun 2020 21:40:43: 4000000 INFO @ Mon, 29 Jun 2020 21:40:46: 11000000 INFO @ Mon, 29 Jun 2020 21:40:47: 16000000 INFO @ Mon, 29 Jun 2020 21:40:48: 5000000 INFO @ Mon, 29 Jun 2020 21:40:50: 12000000 INFO @ Mon, 29 Jun 2020 21:40:53: 17000000 INFO @ Mon, 29 Jun 2020 21:40:53: 6000000 INFO @ Mon, 29 Jun 2020 21:40:55: 13000000 INFO @ Mon, 29 Jun 2020 21:40:56: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:40:56: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:40:56: #1 total tags in treatment: 17585526 INFO @ Mon, 29 Jun 2020 21:40:56: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:40:56: #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 21:40:56: #1 tags after filtering in treatment: 17585526 INFO @ Mon, 29 Jun 2020 21:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:40:56: #1 finished! INFO @ Mon, 29 Jun 2020 21:40:56: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:40:57: #2 number of paired peaks: 206 WARNING @ Mon, 29 Jun 2020 21:40:57: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Mon, 29 Jun 2020 21:40:57: start model_add_line... INFO @ Mon, 29 Jun 2020 21:40:57: start X-correlation... INFO @ Mon, 29 Jun 2020 21:40:57: end of X-cor INFO @ Mon, 29 Jun 2020 21:40:57: #2 finished! INFO @ Mon, 29 Jun 2020 21:40:57: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 21:40:57: #2 alternative fragment length(s) may be 1,39,563,583,585 bps INFO @ Mon, 29 Jun 2020 21:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.05_model.r WARNING @ Mon, 29 Jun 2020 21:40:57: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:40:57: #2 You may need to consider one of the other alternative d(s): 1,39,563,583,585 WARNING @ Mon, 29 Jun 2020 21:40:57: #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 21:40:57: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:40:57: 7000000 INFO @ Mon, 29 Jun 2020 21:41:00: 14000000 INFO @ Mon, 29 Jun 2020 21:41:02: 8000000 INFO @ Mon, 29 Jun 2020 21:41:04: 15000000 INFO @ Mon, 29 Jun 2020 21:41:07: 9000000 INFO @ Mon, 29 Jun 2020 21:41:09: 16000000 INFO @ Mon, 29 Jun 2020 21:41:11: 10000000 INFO @ Mon, 29 Jun 2020 21:41:13: 17000000 INFO @ Mon, 29 Jun 2020 21:41:16: 11000000 INFO @ Mon, 29 Jun 2020 21:41:16: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:41:16: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:41:16: #1 total tags in treatment: 17585526 INFO @ Mon, 29 Jun 2020 21:41:16: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:41:16: #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 21:41:16: #1 tags after filtering in treatment: 17585526 INFO @ Mon, 29 Jun 2020 21:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:41:16: #1 finished! INFO @ Mon, 29 Jun 2020 21:41:16: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:41:18: #2 number of paired peaks: 206 WARNING @ Mon, 29 Jun 2020 21:41:18: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Mon, 29 Jun 2020 21:41:18: start model_add_line... INFO @ Mon, 29 Jun 2020 21:41:18: start X-correlation... INFO @ Mon, 29 Jun 2020 21:41:18: end of X-cor INFO @ Mon, 29 Jun 2020 21:41:18: #2 finished! INFO @ Mon, 29 Jun 2020 21:41:18: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 21:41:18: #2 alternative fragment length(s) may be 1,39,563,583,585 bps INFO @ Mon, 29 Jun 2020 21:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.10_model.r WARNING @ Mon, 29 Jun 2020 21:41:18: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:41:18: #2 You may need to consider one of the other alternative d(s): 1,39,563,583,585 WARNING @ Mon, 29 Jun 2020 21:41:18: #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 21:41:18: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:41:20: 12000000 INFO @ Mon, 29 Jun 2020 21:41:25: 13000000 INFO @ Mon, 29 Jun 2020 21:41:27: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:41:30: 14000000 INFO @ Mon, 29 Jun 2020 21:41:34: 15000000 INFO @ Mon, 29 Jun 2020 21:41:39: 16000000 INFO @ Mon, 29 Jun 2020 21:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.05_summits.bed INFO @ Mon, 29 Jun 2020 21:41:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (697 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:41:43: 17000000 INFO @ Mon, 29 Jun 2020 21:41:46: #1 tag size is determined as 42 bps INFO @ Mon, 29 Jun 2020 21:41:46: #1 tag size = 42 INFO @ Mon, 29 Jun 2020 21:41:46: #1 total tags in treatment: 17585526 INFO @ Mon, 29 Jun 2020 21:41:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:41:46: #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 21:41:46: #1 tags after filtering in treatment: 17585526 INFO @ Mon, 29 Jun 2020 21:41:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:41:46: #1 finished! INFO @ Mon, 29 Jun 2020 21:41:46: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:41:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:41:48: #2 number of paired peaks: 206 WARNING @ Mon, 29 Jun 2020 21:41:48: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Mon, 29 Jun 2020 21:41:48: start model_add_line... INFO @ Mon, 29 Jun 2020 21:41:48: start X-correlation... INFO @ Mon, 29 Jun 2020 21:41:48: end of X-cor INFO @ Mon, 29 Jun 2020 21:41:48: #2 finished! INFO @ Mon, 29 Jun 2020 21:41:48: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 21:41:48: #2 alternative fragment length(s) may be 1,39,563,583,585 bps INFO @ Mon, 29 Jun 2020 21:41:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.20_model.r WARNING @ Mon, 29 Jun 2020 21:41:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:41:48: #2 You may need to consider one of the other alternative d(s): 1,39,563,583,585 WARNING @ Mon, 29 Jun 2020 21:41:48: #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 21:41:48: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:41:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:41:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.10_summits.bed INFO @ Mon, 29 Jun 2020 21:42:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (329 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:42:18: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:42:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:42:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:42:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466543/SRX466543.20_summits.bed INFO @ Mon, 29 Jun 2020 21:42:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (99 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。