Job ID = 6366645 SRX = SRX2144192 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:50 prefetch.2.10.7: 1) Downloading 'SRR4188796'... 2020-06-15T23:31:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:14 prefetch.2.10.7: 'SRR4188796' is valid 2020-06-15T23:32:14 prefetch.2.10.7: 1) 'SRR4188796' was downloaded successfully Read 2717461 spots for SRR4188796/SRR4188796.sra Written 2717461 spots for SRR4188796/SRR4188796.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: 00:00:39 2717461 reads; of these: 2717461 (100.00%) were unpaired; of these: 150964 (5.56%) aligned 0 times 2055701 (75.65%) aligned exactly 1 time 510796 (18.80%) aligned >1 times 94.44% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 136788 / 2566497 = 0.0533 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 08:34:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.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 08:34:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:13: 1000000 INFO @ Tue, 16 Jun 2020 08:34:19: 2000000 INFO @ Tue, 16 Jun 2020 08:34:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:34:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:34:21: #1 total tags in treatment: 2429709 INFO @ Tue, 16 Jun 2020 08:34:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:21: #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 08:34:21: #1 tags after filtering in treatment: 2429709 INFO @ Tue, 16 Jun 2020 08:34:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:21: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:34:21: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:21: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:34:21: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 16 Jun 2020 08:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.05_model.r WARNING @ Tue, 16 Jun 2020 08:34:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:21: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 16 Jun 2020 08:34:21: #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 08:34:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (396 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 @ Tue, 16 Jun 2020 08:34:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.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 08:34:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:43: 1000000 INFO @ Tue, 16 Jun 2020 08:34:48: 2000000 INFO @ Tue, 16 Jun 2020 08:34:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:34:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:34:50: #1 total tags in treatment: 2429709 INFO @ Tue, 16 Jun 2020 08:34:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:50: #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 08:34:50: #1 tags after filtering in treatment: 2429709 INFO @ Tue, 16 Jun 2020 08:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:50: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:34:50: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:50: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:34:50: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 16 Jun 2020 08:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.10_model.r WARNING @ Tue, 16 Jun 2020 08:34:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:50: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 16 Jun 2020 08:34:50: #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 08:34:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (239 records, 4 fields): 2 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 08:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.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 08:35:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:13: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:19: 2000000 INFO @ Tue, 16 Jun 2020 08:35:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:35:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:35:21: #1 total tags in treatment: 2429709 INFO @ Tue, 16 Jun 2020 08:35:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:21: #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 08:35:21: #1 tags after filtering in treatment: 2429709 INFO @ Tue, 16 Jun 2020 08:35:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:21: #2 number of paired peaks: 466 WARNING @ Tue, 16 Jun 2020 08:35:21: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:21: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:35:21: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 16 Jun 2020 08:35:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:21: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 16 Jun 2020 08:35:21: #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 08:35:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144192/SRX2144192.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 millis CompletedMACS2peakCalling