Job ID = 6367517 SRX = SRX331273 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:39:29 prefetch.2.10.7: 1) Downloading 'SRR947508'... 2020-06-15T23:39:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:23 prefetch.2.10.7: 'SRR947508' is valid 2020-06-15T23:40:23 prefetch.2.10.7: 1) 'SRR947508' was downloaded successfully Read 7187826 spots for SRR947508/SRR947508.sra Written 7187826 spots for SRR947508/SRR947508.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: 00:01:10 7187826 reads; of these: 7187826 (100.00%) were unpaired; of these: 287251 (4.00%) aligned 0 times 5912193 (82.25%) aligned exactly 1 time 988382 (13.75%) aligned >1 times 96.00% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 912674 / 6900575 = 0.1323 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 08:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.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 08:43:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:52: 1000000 INFO @ Tue, 16 Jun 2020 08:43:57: 2000000 INFO @ Tue, 16 Jun 2020 08:44:02: 3000000 INFO @ Tue, 16 Jun 2020 08:44:07: 4000000 INFO @ Tue, 16 Jun 2020 08:44:12: 5000000 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 08:44:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:44:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:44:17: #1 total tags in treatment: 5987901 INFO @ Tue, 16 Jun 2020 08:44:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:17: #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 08:44:17: #1 tags after filtering in treatment: 5987901 INFO @ Tue, 16 Jun 2020 08:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:17: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:44:17: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:17: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:44:17: #2 alternative fragment length(s) may be 3,29 bps INFO @ Tue, 16 Jun 2020 08:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.05_model.r WARNING @ Tue, 16 Jun 2020 08:44:17: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:17: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Tue, 16 Jun 2020 08:44:17: #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 08:44:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.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 08:44:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:23: 1000000 INFO @ Tue, 16 Jun 2020 08:44:27: 2000000 INFO @ Tue, 16 Jun 2020 08:44:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:32: 3000000 INFO @ Tue, 16 Jun 2020 08:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.05_summits.bed INFO @ Tue, 16 Jun 2020 08:44:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (462 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:37: 4000000 INFO @ Tue, 16 Jun 2020 08:44:42: 5000000 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 08:44:47: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:44:47: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:44:47: #1 total tags in treatment: 5987901 INFO @ Tue, 16 Jun 2020 08:44:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:47: #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 08:44:47: #1 tags after filtering in treatment: 5987901 INFO @ Tue, 16 Jun 2020 08:44:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:48: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:44:48: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.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 08:44:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:48: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:44:48: #2 alternative fragment length(s) may be 3,29 bps INFO @ Tue, 16 Jun 2020 08:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.10_model.r WARNING @ Tue, 16 Jun 2020 08:44:48: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:48: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Tue, 16 Jun 2020 08:44:48: #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 08:44:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:53: 1000000 INFO @ Tue, 16 Jun 2020 08:44:58: 2000000 INFO @ Tue, 16 Jun 2020 08:45:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:03: 3000000 INFO @ Tue, 16 Jun 2020 08:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.10_summits.bed INFO @ Tue, 16 Jun 2020 08:45:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:08: 4000000 INFO @ Tue, 16 Jun 2020 08:45:13: 5000000 INFO @ Tue, 16 Jun 2020 08:45:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:45:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:45:17: #1 total tags in treatment: 5987901 INFO @ Tue, 16 Jun 2020 08:45:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:17: #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 08:45:17: #1 tags after filtering in treatment: 5987901 INFO @ Tue, 16 Jun 2020 08:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:18: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:45:18: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:18: #2 predicted fragment length is 29 bps INFO @ Tue, 16 Jun 2020 08:45:18: #2 alternative fragment length(s) may be 3,29 bps INFO @ Tue, 16 Jun 2020 08:45:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.20_model.r WARNING @ Tue, 16 Jun 2020 08:45:18: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:18: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Tue, 16 Jun 2020 08:45:18: #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 08:45:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:45:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331273/SRX331273.20_summits.bed INFO @ Tue, 16 Jun 2020 08:45:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling