Job ID = 6497543 SRX = SRX515118 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:28:27 prefetch.2.10.7: 1) Downloading 'SRR1232297'... 2020-06-25T22:28:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:29:00 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:29:00 prefetch.2.10.7: 'SRR1232297' is valid 2020-06-25T22:29:00 prefetch.2.10.7: 1) 'SRR1232297' was downloaded successfully Read 5941311 spots for SRR1232297/SRR1232297.sra Written 5941311 spots for SRR1232297/SRR1232297.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:28 5941311 reads; of these: 5941311 (100.00%) were unpaired; of these: 4731175 (79.63%) aligned 0 times 1009382 (16.99%) aligned exactly 1 time 200754 (3.38%) aligned >1 times 20.37% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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_rmdupse_core] 31063 / 1210136 = 0.0257 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 07:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.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 07:30:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:36: 1000000 INFO @ Fri, 26 Jun 2020 07:30:37: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:30:37: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:30:37: #1 total tags in treatment: 1179073 INFO @ Fri, 26 Jun 2020 07:30:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:30:37: #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 07:30:37: #1 tags after filtering in treatment: 1179073 INFO @ Fri, 26 Jun 2020 07:30:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:30:37: #1 finished! INFO @ Fri, 26 Jun 2020 07:30:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:30:37: #2 number of paired peaks: 309 WARNING @ Fri, 26 Jun 2020 07:30:37: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 26 Jun 2020 07:30:37: start model_add_line... INFO @ Fri, 26 Jun 2020 07:30:37: start X-correlation... INFO @ Fri, 26 Jun 2020 07:30:37: end of X-cor INFO @ Fri, 26 Jun 2020 07:30:37: #2 finished! INFO @ Fri, 26 Jun 2020 07:30:37: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:30:37: #2 alternative fragment length(s) may be 32,187,448,566 bps INFO @ Fri, 26 Jun 2020 07:30:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.05_model.r WARNING @ Fri, 26 Jun 2020 07:30:37: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:30:37: #2 You may need to consider one of the other alternative d(s): 32,187,448,566 WARNING @ Fri, 26 Jun 2020 07:30:37: #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 07:30:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:30:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.05_summits.bed INFO @ Fri, 26 Jun 2020 07:30:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.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 07:31:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:06: 1000000 INFO @ Fri, 26 Jun 2020 07:31:07: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:31:07: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:31:07: #1 total tags in treatment: 1179073 INFO @ Fri, 26 Jun 2020 07:31:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:07: #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 07:31:07: #1 tags after filtering in treatment: 1179073 INFO @ Fri, 26 Jun 2020 07:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:07: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:07: #2 number of paired peaks: 309 WARNING @ Fri, 26 Jun 2020 07:31:07: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:07: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:07: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:07: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:07: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:07: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:31:07: #2 alternative fragment length(s) may be 32,187,448,566 bps INFO @ Fri, 26 Jun 2020 07:31:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.10_model.r WARNING @ Fri, 26 Jun 2020 07:31:07: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:07: #2 You may need to consider one of the other alternative d(s): 32,187,448,566 WARNING @ Fri, 26 Jun 2020 07:31:07: #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 07:31:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:31:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:31:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.10_summits.bed INFO @ Fri, 26 Jun 2020 07:31:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (56 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:31:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.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 07:31:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:31: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:31:36: 1000000 INFO @ Fri, 26 Jun 2020 07:31:37: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 07:31:37: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 07:31:37: #1 total tags in treatment: 1179073 INFO @ Fri, 26 Jun 2020 07:31:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:37: #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 07:31:37: #1 tags after filtering in treatment: 1179073 INFO @ Fri, 26 Jun 2020 07:31:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:31:37: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:37: #2 number of paired peaks: 309 WARNING @ Fri, 26 Jun 2020 07:31:37: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:37: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:37: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:37: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:37: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:37: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:31:37: #2 alternative fragment length(s) may be 32,187,448,566 bps INFO @ Fri, 26 Jun 2020 07:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.20_model.r WARNING @ Fri, 26 Jun 2020 07:31:37: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:37: #2 You may need to consider one of the other alternative d(s): 32,187,448,566 WARNING @ Fri, 26 Jun 2020 07:31:37: #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 07:31:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:31:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX515118/SRX515118.20_summits.bed INFO @ Fri, 26 Jun 2020 07:31:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling