Job ID = 6497445 SRX = SRX494943 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:10:35 prefetch.2.10.7: 1) Downloading 'SRR1198475'... 2020-06-25T22:10:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:13:46 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:13:46 prefetch.2.10.7: 1) 'SRR1198475' was downloaded successfully Read 23003577 spots for SRR1198475/SRR1198475.sra Written 23003577 spots for SRR1198475/SRR1198475.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: 00:05:05 23003577 reads; of these: 23003577 (100.00%) were unpaired; of these: 1607461 (6.99%) aligned 0 times 17615677 (76.58%) aligned exactly 1 time 3780439 (16.43%) aligned >1 times 93.01% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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_rmdupse_core] 13810762 / 21396116 = 0.6455 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 07:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.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 07:23:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:23:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:23:55: 1000000 INFO @ Fri, 26 Jun 2020 07:24:01: 2000000 INFO @ Fri, 26 Jun 2020 07:24:07: 3000000 INFO @ Fri, 26 Jun 2020 07:24:12: 4000000 INFO @ Fri, 26 Jun 2020 07:24:18: 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 @ Fri, 26 Jun 2020 07:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.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 07:24:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:24:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:24:24: 6000000 INFO @ Fri, 26 Jun 2020 07:24:25: 1000000 INFO @ Fri, 26 Jun 2020 07:24:29: 7000000 INFO @ Fri, 26 Jun 2020 07:24:30: 2000000 INFO @ Fri, 26 Jun 2020 07:24:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:24:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:24:33: #1 total tags in treatment: 7585354 INFO @ Fri, 26 Jun 2020 07:24:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:24:33: #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 07:24:33: #1 tags after filtering in treatment: 7585354 INFO @ Fri, 26 Jun 2020 07:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:24:33: #1 finished! INFO @ Fri, 26 Jun 2020 07:24:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:24:33: #2 number of paired peaks: 637 WARNING @ Fri, 26 Jun 2020 07:24:33: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Fri, 26 Jun 2020 07:24:33: start model_add_line... INFO @ Fri, 26 Jun 2020 07:24:33: start X-correlation... INFO @ Fri, 26 Jun 2020 07:24:33: end of X-cor INFO @ Fri, 26 Jun 2020 07:24:33: #2 finished! INFO @ Fri, 26 Jun 2020 07:24:33: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:24:33: #2 alternative fragment length(s) may be 2,45,542 bps INFO @ Fri, 26 Jun 2020 07:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.05_model.r INFO @ Fri, 26 Jun 2020 07:24:36: 3000000 INFO @ Fri, 26 Jun 2020 07:24:41: 4000000 WARNING @ Fri, 26 Jun 2020 07:24:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:24:43: #2 You may need to consider one of the other alternative d(s): 2,45,542 WARNING @ Fri, 26 Jun 2020 07:24:43: #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 07:24:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:24:46: 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 @ Fri, 26 Jun 2020 07:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.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 07:24:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:24:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:24:51: 6000000 INFO @ Fri, 26 Jun 2020 07:24:56: 1000000 INFO @ Fri, 26 Jun 2020 07:24:56: 7000000 INFO @ Fri, 26 Jun 2020 07:24:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:25:00: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:25:00: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:25:00: #1 total tags in treatment: 7585354 INFO @ Fri, 26 Jun 2020 07:25:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:25:00: #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 07:25:00: #1 tags after filtering in treatment: 7585354 INFO @ Fri, 26 Jun 2020 07:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:25:00: #1 finished! INFO @ Fri, 26 Jun 2020 07:25:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:25:00: #2 number of paired peaks: 637 WARNING @ Fri, 26 Jun 2020 07:25:00: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Fri, 26 Jun 2020 07:25:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:25:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:25:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:25:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:25:00: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:25:00: #2 alternative fragment length(s) may be 2,45,542 bps INFO @ Fri, 26 Jun 2020 07:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.10_model.r INFO @ Fri, 26 Jun 2020 07:25:01: 2000000 INFO @ Fri, 26 Jun 2020 07:25:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:25:07: 3000000 INFO @ Fri, 26 Jun 2020 07:25:13: 4000000 INFO @ Fri, 26 Jun 2020 07:25:18: 5000000 BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 07:25:24: 6000000 INFO @ Fri, 26 Jun 2020 07:25:30: 7000000 INFO @ Fri, 26 Jun 2020 07:25:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:25:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:25:33: #1 total tags in treatment: 7585354 INFO @ Fri, 26 Jun 2020 07:25:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:25:33: #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 07:25:33: #1 tags after filtering in treatment: 7585354 INFO @ Fri, 26 Jun 2020 07:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:25:33: #1 finished! INFO @ Fri, 26 Jun 2020 07:25:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:25:34: #2 number of paired peaks: 637 WARNING @ Fri, 26 Jun 2020 07:25:34: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Fri, 26 Jun 2020 07:25:34: start model_add_line... INFO @ Fri, 26 Jun 2020 07:25:34: start X-correlation... INFO @ Fri, 26 Jun 2020 07:25:34: end of X-cor INFO @ Fri, 26 Jun 2020 07:25:34: #2 finished! INFO @ Fri, 26 Jun 2020 07:25:34: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 07:25:34: #2 alternative fragment length(s) may be 2,45,542 bps INFO @ Fri, 26 Jun 2020 07:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.20_model.r WARNING @ Fri, 26 Jun 2020 07:25:34: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:25:34: #2 You may need to consider one of the other alternative d(s): 2,45,542 WARNING @ Fri, 26 Jun 2020 07:25:34: #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 07:25:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:25:34: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 26 Jun 2020 07:25:34: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:25:34: #2 You may need to consider one of the other alternative d(s): 2,45,542 WARNING @ Fri, 26 Jun 2020 07:25:34: #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 07:25:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.05_peaks.narrowPeak BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.05_summits.bed INFO @ Fri, 26 Jun 2020 07:25:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (839 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:25:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:25:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:25:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.20_summits.bed INFO @ Fri, 26 Jun 2020 07:25:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (268 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494943/SRX494943.10_summits.bed INFO @ Fri, 26 Jun 2020 07:25:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (581 records, 4 fields): 2 millis CompletedMACS2peakCalling