Job ID = 6368374 SRX = SRX495054 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:15:21 prefetch.2.10.7: 1) Downloading 'SRR1198586'... 2020-06-16T00:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:19:02 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:19:02 prefetch.2.10.7: 1) 'SRR1198586' was downloaded successfully Read 13809537 spots for SRR1198586/SRR1198586.sra Written 13809537 spots for SRR1198586/SRR1198586.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:15 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2268840 (16.43%) aligned 0 times 9710130 (70.31%) aligned exactly 1 time 1830567 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 1988389 / 11540697 = 0.1723 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 09:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.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 09:24:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:01: 1000000 INFO @ Tue, 16 Jun 2020 09:25:06: 2000000 INFO @ Tue, 16 Jun 2020 09:25:11: 3000000 INFO @ Tue, 16 Jun 2020 09:25:16: 4000000 INFO @ Tue, 16 Jun 2020 09:25:21: 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 09:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.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 09:25:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:25: 6000000 INFO @ Tue, 16 Jun 2020 09:25:30: 1000000 INFO @ Tue, 16 Jun 2020 09:25:30: 7000000 INFO @ Tue, 16 Jun 2020 09:25:35: 2000000 INFO @ Tue, 16 Jun 2020 09:25:35: 8000000 INFO @ Tue, 16 Jun 2020 09:25:40: 3000000 INFO @ Tue, 16 Jun 2020 09:25:40: 9000000 INFO @ Tue, 16 Jun 2020 09:25:43: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:25:43: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:25:43: #1 total tags in treatment: 9552308 INFO @ Tue, 16 Jun 2020 09:25:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:43: #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 09:25:43: #1 tags after filtering in treatment: 9552308 INFO @ Tue, 16 Jun 2020 09:25:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:44: #2 number of paired peaks: 277 WARNING @ Tue, 16 Jun 2020 09:25:44: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:44: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:25:44: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 16 Jun 2020 09:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.05_model.r WARNING @ Tue, 16 Jun 2020 09:25:44: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:44: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 16 Jun 2020 09:25:44: #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 09:25:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:45: 4000000 INFO @ Tue, 16 Jun 2020 09:25:50: 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 09:25:55: 6000000 INFO @ Tue, 16 Jun 2020 09:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.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 09:25:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:00: 7000000 INFO @ Tue, 16 Jun 2020 09:26:01: 1000000 INFO @ Tue, 16 Jun 2020 09:26:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:05: 8000000 INFO @ Tue, 16 Jun 2020 09:26:06: 2000000 INFO @ Tue, 16 Jun 2020 09:26:10: 9000000 INFO @ Tue, 16 Jun 2020 09:26:11: 3000000 INFO @ Tue, 16 Jun 2020 09:26:13: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:13: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:13: #1 total tags in treatment: 9552308 INFO @ Tue, 16 Jun 2020 09:26:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:13: #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 09:26:13: #1 tags after filtering in treatment: 9552308 INFO @ Tue, 16 Jun 2020 09:26:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (572 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:14: #2 number of paired peaks: 277 WARNING @ Tue, 16 Jun 2020 09:26:14: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:14: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:26:14: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 16 Jun 2020 09:26:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:14: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:14: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 16 Jun 2020 09:26:14: #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 09:26:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:16: 4000000 INFO @ Tue, 16 Jun 2020 09:26:22: 5000000 INFO @ Tue, 16 Jun 2020 09:26:27: 6000000 INFO @ Tue, 16 Jun 2020 09:26:32: 7000000 INFO @ Tue, 16 Jun 2020 09:26:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:36: 8000000 INFO @ Tue, 16 Jun 2020 09:26:41: 9000000 INFO @ Tue, 16 Jun 2020 09:26:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (306 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:44: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:44: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:44: #1 total tags in treatment: 9552308 INFO @ Tue, 16 Jun 2020 09:26:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:44: #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 09:26:44: #1 tags after filtering in treatment: 9552308 INFO @ Tue, 16 Jun 2020 09:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:45: #2 number of paired peaks: 277 WARNING @ Tue, 16 Jun 2020 09:26:45: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:45: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:26:45: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 16 Jun 2020 09:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.20_model.r WARNING @ Tue, 16 Jun 2020 09:26:45: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:45: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 16 Jun 2020 09:26:45: #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 09:26:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:45: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:27:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495054/SRX495054.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (111 records, 4 fields): 1 millis CompletedMACS2peakCalling