Job ID = 6366301 SRX = SRX1078725 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:34:21 prefetch.2.10.7: 1) Downloading 'SRR2084332'... 2020-06-15T22:34:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:36:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:36:18 prefetch.2.10.7: 1) 'SRR2084332' was downloaded successfully Read 16373975 spots for SRR2084332/SRR2084332.sra Written 16373975 spots for SRR2084332/SRR2084332.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: 00:00:01 Multiseed full-index search: 00:03:05 16373975 reads; of these: 16373975 (100.00%) were unpaired; of these: 6161134 (37.63%) aligned 0 times 8474484 (51.76%) aligned exactly 1 time 1738357 (10.62%) aligned >1 times 62.37% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7376750 / 10212841 = 0.7223 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 07:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.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 07:42:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:42: 1000000 INFO @ Tue, 16 Jun 2020 07:42:47: 2000000 INFO @ Tue, 16 Jun 2020 07:42:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:42:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:42:52: #1 total tags in treatment: 2836091 INFO @ Tue, 16 Jun 2020 07:42:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:52: #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 07:42:52: #1 tags after filtering in treatment: 2836091 INFO @ Tue, 16 Jun 2020 07:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:52: #2 number of paired peaks: 842 WARNING @ Tue, 16 Jun 2020 07:42:52: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Tue, 16 Jun 2020 07:42:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:52: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:42:52: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 16 Jun 2020 07:42:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.05_model.r WARNING @ Tue, 16 Jun 2020 07:42:52: #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 07:42:52: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 16 Jun 2020 07:42:52: #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 07:42:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.05_summits.bed INFO @ Tue, 16 Jun 2020 07:43:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (760 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 07:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.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 07:43:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:12: 1000000 INFO @ Tue, 16 Jun 2020 07:43:17: 2000000 INFO @ Tue, 16 Jun 2020 07:43:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:21: #1 total tags in treatment: 2836091 INFO @ Tue, 16 Jun 2020 07:43:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:21: #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 07:43:21: #1 tags after filtering in treatment: 2836091 INFO @ Tue, 16 Jun 2020 07:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:21: #2 number of paired peaks: 842 WARNING @ Tue, 16 Jun 2020 07:43:21: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:21: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:43:21: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 16 Jun 2020 07:43:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.10_model.r WARNING @ Tue, 16 Jun 2020 07:43:21: #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 07:43:21: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 16 Jun 2020 07:43:21: #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 07:43:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.10_summits.bed INFO @ Tue, 16 Jun 2020 07:43:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (499 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 07:43:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.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 07:43:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:42: 1000000 INFO @ Tue, 16 Jun 2020 07:43:47: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:43:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:52: #1 total tags in treatment: 2836091 INFO @ Tue, 16 Jun 2020 07:43:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:52: #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 07:43:52: #1 tags after filtering in treatment: 2836091 INFO @ Tue, 16 Jun 2020 07:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:52: #2 number of paired peaks: 842 WARNING @ Tue, 16 Jun 2020 07:43:52: Fewer paired peaks (842) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 842 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:52: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 07:43:52: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 16 Jun 2020 07:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.20_model.r WARNING @ Tue, 16 Jun 2020 07:43:52: #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 07:43:52: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 16 Jun 2020 07:43:52: #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 07:43:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:43:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078725/SRX1078725.20_summits.bed INFO @ Tue, 16 Jun 2020 07:44:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (236 records, 4 fields): 1 millis CompletedMACS2peakCalling