Job ID = 6366160 SRX = SRX065685 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:49:07 prefetch.2.10.7: 1) Downloading 'SRR217391'... 2020-06-15T22:49:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:36 prefetch.2.10.7: 'SRR217391' is valid 2020-06-15T22:49:36 prefetch.2.10.7: 1) 'SRR217391' was downloaded successfully Read 4949042 spots for SRR217391/SRR217391.sra Written 4949042 spots for SRR217391/SRR217391.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: 00:00:37 4949042 reads; of these: 4949042 (100.00%) were unpaired; of these: 1669544 (33.73%) aligned 0 times 2705285 (54.66%) aligned exactly 1 time 574213 (11.60%) aligned >1 times 66.27% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 177531 / 3279498 = 0.0541 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 07:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.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 07:51:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:45: 1000000 INFO @ Tue, 16 Jun 2020 07:51:51: 2000000 INFO @ Tue, 16 Jun 2020 07:51:56: 3000000 INFO @ Tue, 16 Jun 2020 07:51:57: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:51:57: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:51:57: #1 total tags in treatment: 3101967 INFO @ Tue, 16 Jun 2020 07:51:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:57: #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 07:51:57: #1 tags after filtering in treatment: 3101967 INFO @ Tue, 16 Jun 2020 07:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:57: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 07:51:57: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:57: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:57: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:57: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:57: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:57: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:51:57: #2 alternative fragment length(s) may be 4,33 bps INFO @ Tue, 16 Jun 2020 07:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.05_model.r WARNING @ Tue, 16 Jun 2020 07:51:57: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:57: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Tue, 16 Jun 2020 07:51:57: #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 07:51:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:07: Done! 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 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.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 07:52:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:15: 1000000 INFO @ Tue, 16 Jun 2020 07:52:20: 2000000 INFO @ Tue, 16 Jun 2020 07:52:25: 3000000 INFO @ Tue, 16 Jun 2020 07:52:25: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:52:25: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:52:25: #1 total tags in treatment: 3101967 INFO @ Tue, 16 Jun 2020 07:52:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:25: #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 07:52:25: #1 tags after filtering in treatment: 3101967 INFO @ Tue, 16 Jun 2020 07:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:25: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:26: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 07:52:26: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:26: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:52:26: #2 alternative fragment length(s) may be 4,33 bps INFO @ Tue, 16 Jun 2020 07:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:26: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:26: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Tue, 16 Jun 2020 07:52:26: #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 07:52:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.10_summits.bed INFO @ Tue, 16 Jun 2020 07:52:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (187 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 @ Tue, 16 Jun 2020 07:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.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 07:52:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:45: 1000000 INFO @ Tue, 16 Jun 2020 07:52:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:55: 3000000 INFO @ Tue, 16 Jun 2020 07:52:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:52:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:52:55: #1 total tags in treatment: 3101967 INFO @ Tue, 16 Jun 2020 07:52:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:55: #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 07:52:56: #1 tags after filtering in treatment: 3101967 INFO @ Tue, 16 Jun 2020 07:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:56: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 07:52:56: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:56: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:52:56: #2 alternative fragment length(s) may be 4,33 bps INFO @ Tue, 16 Jun 2020 07:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.20_model.r WARNING @ Tue, 16 Jun 2020 07:52:56: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:56: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Tue, 16 Jun 2020 07:52:56: #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 07:52:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:53:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065685/SRX065685.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (55 records, 4 fields): 1 millis CompletedMACS2peakCalling