Job ID = 6367231 SRX = SRX3043417 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:21:31 prefetch.2.10.7: 1) Downloading 'SRR5875901'... 2020-06-15T23:21:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:14 prefetch.2.10.7: 1) 'SRR5875901' was downloaded successfully 2020-06-15T23:24:14 prefetch.2.10.7: 'SRR5875901' has 0 unresolved dependencies Read 41967833 spots for SRR5875901/SRR5875901.sra Written 41967833 spots for SRR5875901/SRR5875901.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: 00:06:17 41967833 reads; of these: 41967833 (100.00%) were unpaired; of these: 34651749 (82.57%) aligned 0 times 6270148 (14.94%) aligned exactly 1 time 1045936 (2.49%) aligned >1 times 17.43% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 685393 / 7316084 = 0.0937 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 08:35:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.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 08:35:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:21: 1000000 INFO @ Tue, 16 Jun 2020 08:35:26: 2000000 INFO @ Tue, 16 Jun 2020 08:35:32: 3000000 INFO @ Tue, 16 Jun 2020 08:35:37: 4000000 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 08:35:43: 5000000 INFO @ Tue, 16 Jun 2020 08:35:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.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 08:35:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:49: 6000000 INFO @ Tue, 16 Jun 2020 08:35:51: 1000000 INFO @ Tue, 16 Jun 2020 08:35:53: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:35:53: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:35:53: #1 total tags in treatment: 6630691 INFO @ Tue, 16 Jun 2020 08:35:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:53: #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 08:35:53: #1 tags after filtering in treatment: 6630691 INFO @ Tue, 16 Jun 2020 08:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:54: #2 number of paired peaks: 824 WARNING @ Tue, 16 Jun 2020 08:35:54: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:54: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:35:54: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 16 Jun 2020 08:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.05_model.r WARNING @ Tue, 16 Jun 2020 08:35:54: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:54: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 16 Jun 2020 08:35:54: #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 08:35:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:57: 2000000 INFO @ Tue, 16 Jun 2020 08:36:03: 3000000 INFO @ Tue, 16 Jun 2020 08:36:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:09: 4000000 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 08:36:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.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 08:36:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3095 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:15: 5000000 INFO @ Tue, 16 Jun 2020 08:36:22: 6000000 INFO @ Tue, 16 Jun 2020 08:36:22: 1000000 INFO @ Tue, 16 Jun 2020 08:36:27: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:36:27: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:36:27: #1 total tags in treatment: 6630691 INFO @ Tue, 16 Jun 2020 08:36:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:27: #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 08:36:27: #1 tags after filtering in treatment: 6630691 INFO @ Tue, 16 Jun 2020 08:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:27: #2 number of paired peaks: 824 WARNING @ Tue, 16 Jun 2020 08:36:27: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:27: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:36:27: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 16 Jun 2020 08:36:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:27: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:27: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 16 Jun 2020 08:36:27: #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 08:36:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:30: 2000000 INFO @ Tue, 16 Jun 2020 08:36:37: 3000000 INFO @ Tue, 16 Jun 2020 08:36:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:44: 4000000 INFO @ Tue, 16 Jun 2020 08:36:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.10_summits.bed INFO @ Tue, 16 Jun 2020 08:36:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1906 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:51: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:58: 6000000 INFO @ Tue, 16 Jun 2020 08:37:02: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:37:02: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:37:02: #1 total tags in treatment: 6630691 INFO @ Tue, 16 Jun 2020 08:37:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:02: #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 08:37:02: #1 tags after filtering in treatment: 6630691 INFO @ Tue, 16 Jun 2020 08:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:02: #2 number of paired peaks: 824 WARNING @ Tue, 16 Jun 2020 08:37:02: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:02: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:37:02: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 16 Jun 2020 08:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.20_model.r WARNING @ Tue, 16 Jun 2020 08:37:02: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:02: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 16 Jun 2020 08:37:02: #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 08:37:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043417/SRX3043417.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (710 records, 4 fields): 2 millis CompletedMACS2peakCalling