Job ID = 6369019 SRX = SRX982085 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:47:24 prefetch.2.10.7: 1) Downloading 'SRR1956572'... 2020-06-16T00:47:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:48:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:48:58 prefetch.2.10.7: 'SRR1956572' is valid 2020-06-16T00:48:58 prefetch.2.10.7: 1) 'SRR1956572' was downloaded successfully Read 10867984 spots for SRR1956572/SRR1956572.sra Written 10867984 spots for SRR1956572/SRR1956572.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: 00:02:26 10867984 reads; of these: 10867984 (100.00%) were unpaired; of these: 475065 (4.37%) aligned 0 times 8415457 (77.43%) aligned exactly 1 time 1977462 (18.20%) aligned >1 times 95.63% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 1009076 / 10392919 = 0.0971 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 09:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.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 09:55:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:10: 1000000 INFO @ Tue, 16 Jun 2020 09:55:16: 2000000 INFO @ Tue, 16 Jun 2020 09:55:22: 3000000 INFO @ Tue, 16 Jun 2020 09:55:28: 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 09:55:34: 5000000 INFO @ Tue, 16 Jun 2020 09:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.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 09:55:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:40: 6000000 INFO @ Tue, 16 Jun 2020 09:55:41: 1000000 INFO @ Tue, 16 Jun 2020 09:55:47: 7000000 INFO @ Tue, 16 Jun 2020 09:55:48: 2000000 INFO @ Tue, 16 Jun 2020 09:55:54: 8000000 INFO @ Tue, 16 Jun 2020 09:55:55: 3000000 INFO @ Tue, 16 Jun 2020 09:56:01: 9000000 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 09:56:02: 4000000 INFO @ Tue, 16 Jun 2020 09:56:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:56:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:56:04: #1 total tags in treatment: 9383843 INFO @ Tue, 16 Jun 2020 09:56:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:04: #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 09:56:04: #1 tags after filtering in treatment: 9383843 INFO @ Tue, 16 Jun 2020 09:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.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 09:56:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:05: #2 number of paired peaks: 420 WARNING @ Tue, 16 Jun 2020 09:56:05: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:05: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:56:05: #2 alternative fragment length(s) may be 4,57 bps INFO @ Tue, 16 Jun 2020 09:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.05_model.r WARNING @ Tue, 16 Jun 2020 09:56:05: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:05: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Tue, 16 Jun 2020 09:56:05: #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 09:56:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:10: 5000000 INFO @ Tue, 16 Jun 2020 09:56:11: 1000000 INFO @ Tue, 16 Jun 2020 09:56:17: 6000000 INFO @ Tue, 16 Jun 2020 09:56:18: 2000000 INFO @ Tue, 16 Jun 2020 09:56:24: 7000000 INFO @ Tue, 16 Jun 2020 09:56:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:25: 3000000 INFO @ Tue, 16 Jun 2020 09:56:31: 8000000 INFO @ Tue, 16 Jun 2020 09:56:31: 4000000 INFO @ Tue, 16 Jun 2020 09:56:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.05_summits.bed INFO @ Tue, 16 Jun 2020 09:56:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1155 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:38: 9000000 INFO @ Tue, 16 Jun 2020 09:56:38: 5000000 INFO @ Tue, 16 Jun 2020 09:56:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:56:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:56:41: #1 total tags in treatment: 9383843 INFO @ Tue, 16 Jun 2020 09:56:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:41: #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 09:56:41: #1 tags after filtering in treatment: 9383843 INFO @ Tue, 16 Jun 2020 09:56:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:42: #2 number of paired peaks: 420 WARNING @ Tue, 16 Jun 2020 09:56:42: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:42: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:56:42: #2 alternative fragment length(s) may be 4,57 bps INFO @ Tue, 16 Jun 2020 09:56:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.10_model.r WARNING @ Tue, 16 Jun 2020 09:56:42: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:42: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Tue, 16 Jun 2020 09:56:42: #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 09:56:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:45: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:56:50: 7000000 INFO @ Tue, 16 Jun 2020 09:56:56: 8000000 INFO @ Tue, 16 Jun 2020 09:57:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:02: 9000000 INFO @ Tue, 16 Jun 2020 09:57:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:57:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:57:04: #1 total tags in treatment: 9383843 INFO @ Tue, 16 Jun 2020 09:57:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:04: #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 09:57:05: #1 tags after filtering in treatment: 9383843 INFO @ Tue, 16 Jun 2020 09:57:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:05: #2 number of paired peaks: 420 WARNING @ Tue, 16 Jun 2020 09:57:05: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:05: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:57:05: #2 alternative fragment length(s) may be 4,57 bps INFO @ Tue, 16 Jun 2020 09:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:05: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:05: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Tue, 16 Jun 2020 09:57:05: #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 09:57:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.10_summits.bed INFO @ Tue, 16 Jun 2020 09:57:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (447 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982085/SRX982085.20_summits.bed INFO @ Tue, 16 Jun 2020 09:57:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling