Job ID = 6366790 SRX = SRX233455 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:08 prefetch.2.10.7: 1) Downloading 'SRR701511'... 2020-06-15T23:04:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:32 prefetch.2.10.7: 'SRR701511' is valid 2020-06-15T23:04:32 prefetch.2.10.7: 1) 'SRR701511' was downloaded successfully Read 6482158 spots for SRR701511/SRR701511.sra Written 6482158 spots for SRR701511/SRR701511.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: 00:00:58 6482158 reads; of these: 6482158 (100.00%) were unpaired; of these: 1174709 (18.12%) aligned 0 times 4429811 (68.34%) aligned exactly 1 time 877638 (13.54%) aligned >1 times 81.88% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 326248 / 5307449 = 0.0615 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 08:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.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 08:07:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:27: 1000000 INFO @ Tue, 16 Jun 2020 08:07:32: 2000000 INFO @ Tue, 16 Jun 2020 08:07:37: 3000000 INFO @ Tue, 16 Jun 2020 08:07:43: 4000000 INFO @ Tue, 16 Jun 2020 08:07:48: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:07:48: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:07:48: #1 total tags in treatment: 4981201 INFO @ Tue, 16 Jun 2020 08:07:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:48: #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 08:07:48: #1 tags after filtering in treatment: 4981201 INFO @ Tue, 16 Jun 2020 08:07:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:48: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 08:07:48: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:48: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:07:48: #2 alternative fragment length(s) may be 3,35,528,570,582 bps INFO @ Tue, 16 Jun 2020 08:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.05_model.r WARNING @ Tue, 16 Jun 2020 08:07:48: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:48: #2 You may need to consider one of the other alternative d(s): 3,35,528,570,582 WARNING @ Tue, 16 Jun 2020 08:07:48: #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 08:07:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:48: #3 Pre-compute pvalue-qvalue table... 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 08:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.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 08:07:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:57: 1000000 INFO @ Tue, 16 Jun 2020 08:07:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:02: 2000000 INFO @ Tue, 16 Jun 2020 08:08:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (511 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:07: 3000000 INFO @ Tue, 16 Jun 2020 08:08:12: 4000000 INFO @ Tue, 16 Jun 2020 08:08:17: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:17: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:17: #1 total tags in treatment: 4981201 INFO @ Tue, 16 Jun 2020 08:08:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:17: #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 08:08:17: #1 tags after filtering in treatment: 4981201 INFO @ Tue, 16 Jun 2020 08:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:18: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 08:08:18: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:18: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:08:18: #2 alternative fragment length(s) may be 3,35,528,570,582 bps INFO @ Tue, 16 Jun 2020 08:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.10_model.r WARNING @ Tue, 16 Jun 2020 08:08:18: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:18: #2 You may need to consider one of the other alternative d(s): 3,35,528,570,582 WARNING @ Tue, 16 Jun 2020 08:08:18: #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 08:08:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:18: #3 Pre-compute pvalue-qvalue table... 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 08:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.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 08:08:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:29: 1000000 INFO @ Tue, 16 Jun 2020 08:08:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (228 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:35: 2000000 INFO @ Tue, 16 Jun 2020 08:08:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:49: 4000000 INFO @ Tue, 16 Jun 2020 08:08:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:55: #1 total tags in treatment: 4981201 INFO @ Tue, 16 Jun 2020 08:08:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:55: #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 08:08:55: #1 tags after filtering in treatment: 4981201 INFO @ Tue, 16 Jun 2020 08:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:56: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 08:08:56: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:56: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:08:56: #2 alternative fragment length(s) may be 3,35,528,570,582 bps INFO @ Tue, 16 Jun 2020 08:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.20_model.r WARNING @ Tue, 16 Jun 2020 08:08:56: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:56: #2 You may need to consider one of the other alternative d(s): 3,35,528,570,582 WARNING @ Tue, 16 Jun 2020 08:08:56: #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 08:08:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233455/SRX233455.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling