Job ID = 6368529 SRX = SRX5020758 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:16:06 prefetch.2.10.7: 1) Downloading 'SRR8201381'... 2020-06-16T00:16:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:44 prefetch.2.10.7: 'SRR8201381' is valid 2020-06-16T00:16:44 prefetch.2.10.7: 1) 'SRR8201381' was downloaded successfully Read 6143335 spots for SRR8201381/SRR8201381.sra Written 6143335 spots for SRR8201381/SRR8201381.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: 00:01:17 6143335 reads; of these: 6143335 (100.00%) were unpaired; of these: 191923 (3.12%) aligned 0 times 4928875 (80.23%) aligned exactly 1 time 1022537 (16.64%) aligned >1 times 96.88% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 340533 / 5951412 = 0.0572 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 @ Tue, 16 Jun 2020 09:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.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 @ Tue, 16 Jun 2020 09:20:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:01: 1000000 INFO @ Tue, 16 Jun 2020 09:21:06: 2000000 INFO @ Tue, 16 Jun 2020 09:21:11: 3000000 INFO @ Tue, 16 Jun 2020 09:21:16: 4000000 INFO @ Tue, 16 Jun 2020 09:21:22: 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 @ Tue, 16 Jun 2020 09:21:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:25: #1 total tags in treatment: 5610879 INFO @ Tue, 16 Jun 2020 09:21:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:21:25: #1 tags after filtering in treatment: 5610879 INFO @ Tue, 16 Jun 2020 09:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:25: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:21:25: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:25: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:21:25: #2 alternative fragment length(s) may be 55,571 bps INFO @ Tue, 16 Jun 2020 09:21:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.05_model.r WARNING @ Tue, 16 Jun 2020 09:21:25: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:25: #2 You may need to consider one of the other alternative d(s): 55,571 WARNING @ Tue, 16 Jun 2020 09:21:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:21:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.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 @ Tue, 16 Jun 2020 09:21:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:31: 1000000 INFO @ Tue, 16 Jun 2020 09:21:36: 2000000 INFO @ Tue, 16 Jun 2020 09:21:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:41: 3000000 INFO @ Tue, 16 Jun 2020 09:21:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.05_summits.bed INFO @ Tue, 16 Jun 2020 09:21:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:46: 4000000 INFO @ Tue, 16 Jun 2020 09:21:51: 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 @ Tue, 16 Jun 2020 09:21:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:54: #1 total tags in treatment: 5610879 INFO @ Tue, 16 Jun 2020 09:21:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:21:54: #1 tags after filtering in treatment: 5610879 INFO @ Tue, 16 Jun 2020 09:21:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:55: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:21:55: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:55: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:21:55: #2 alternative fragment length(s) may be 55,571 bps INFO @ Tue, 16 Jun 2020 09:21:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.10_model.r WARNING @ Tue, 16 Jun 2020 09:21:55: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:55: #2 You may need to consider one of the other alternative d(s): 55,571 WARNING @ Tue, 16 Jun 2020 09:21:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:21:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.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 @ Tue, 16 Jun 2020 09:21:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:01: 1000000 INFO @ Tue, 16 Jun 2020 09:22:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:06: 2000000 INFO @ Tue, 16 Jun 2020 09:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:11: 3000000 INFO @ Tue, 16 Jun 2020 09:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.10_summits.bed INFO @ Tue, 16 Jun 2020 09:22:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:16: 4000000 INFO @ Tue, 16 Jun 2020 09:22:21: 5000000 INFO @ Tue, 16 Jun 2020 09:22:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:22:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:22:24: #1 total tags in treatment: 5610879 INFO @ Tue, 16 Jun 2020 09:22:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:22:24: #1 tags after filtering in treatment: 5610879 INFO @ Tue, 16 Jun 2020 09:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:25: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:22:25: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:25: #2 predicted fragment length is 55 bps INFO @ Tue, 16 Jun 2020 09:22:25: #2 alternative fragment length(s) may be 55,571 bps INFO @ Tue, 16 Jun 2020 09:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.20_model.r WARNING @ Tue, 16 Jun 2020 09:22:25: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:25: #2 You may need to consider one of the other alternative d(s): 55,571 WARNING @ Tue, 16 Jun 2020 09:22:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:22:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:22:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020758/SRX5020758.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (118 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。