Job ID = 6369016 SRX = SRX982082 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:44:12 prefetch.2.10.7: 1) Downloading 'SRR1956567'... 2020-06-16T00:44:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:31 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:31 prefetch.2.10.7: 'SRR1956567' is valid 2020-06-16T00:45:31 prefetch.2.10.7: 1) 'SRR1956567' was downloaded successfully Read 4834751 spots for SRR1956567/SRR1956567.sra Written 4834751 spots for SRR1956567/SRR1956567.sra 2020-06-16T00:45:57 prefetch.2.10.7: 1) Downloading 'SRR1956568'... 2020-06-16T00:45:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:47:01 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:47:01 prefetch.2.10.7: 'SRR1956568' is valid 2020-06-16T00:47:01 prefetch.2.10.7: 1) 'SRR1956568' was downloaded successfully Read 5972442 spots for SRR1956568/SRR1956568.sra Written 5972442 spots for SRR1956568/SRR1956568.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 10807193 reads; of these: 10807193 (100.00%) were unpaired; of these: 760066 (7.03%) aligned 0 times 8346853 (77.23%) aligned exactly 1 time 1700274 (15.73%) aligned >1 times 92.97% 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] 676185 / 10047127 = 0.0673 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 09:53:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.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 09:53:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:28: 1000000 INFO @ Tue, 16 Jun 2020 09:53:34: 2000000 INFO @ Tue, 16 Jun 2020 09:53:40: 3000000 INFO @ Tue, 16 Jun 2020 09:53:46: 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 09:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.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 09:53:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:52: 5000000 INFO @ Tue, 16 Jun 2020 09:53:58: 6000000 INFO @ Tue, 16 Jun 2020 09:53:58: 1000000 INFO @ Tue, 16 Jun 2020 09:54:04: 7000000 INFO @ Tue, 16 Jun 2020 09:54:04: 2000000 INFO @ Tue, 16 Jun 2020 09:54:10: 3000000 INFO @ Tue, 16 Jun 2020 09:54:10: 8000000 INFO @ Tue, 16 Jun 2020 09:54:16: 9000000 INFO @ Tue, 16 Jun 2020 09:54:16: 4000000 INFO @ Tue, 16 Jun 2020 09:54:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:19: #1 total tags in treatment: 9370942 INFO @ Tue, 16 Jun 2020 09:54:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:19: #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 09:54:19: #1 tags after filtering in treatment: 9370942 INFO @ Tue, 16 Jun 2020 09:54:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:19: #2 number of paired peaks: 302 WARNING @ Tue, 16 Jun 2020 09:54:19: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:20: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:54:20: #2 alternative fragment length(s) may be 4,47,595 bps INFO @ Tue, 16 Jun 2020 09:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.05_model.r WARNING @ Tue, 16 Jun 2020 09:54:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:20: #2 You may need to consider one of the other alternative d(s): 4,47,595 WARNING @ Tue, 16 Jun 2020 09:54:20: #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 09:54:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:20: #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 09:54:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.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 09:54:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:23: 5000000 INFO @ Tue, 16 Jun 2020 09:54:30: 1000000 INFO @ Tue, 16 Jun 2020 09:54:30: 6000000 INFO @ Tue, 16 Jun 2020 09:54:37: 7000000 INFO @ Tue, 16 Jun 2020 09:54:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:38: 2000000 INFO @ Tue, 16 Jun 2020 09:54:45: 8000000 INFO @ Tue, 16 Jun 2020 09:54:46: 3000000 INFO @ Tue, 16 Jun 2020 09:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.05_summits.bed INFO @ Tue, 16 Jun 2020 09:54:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (597 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:52: 9000000 INFO @ Tue, 16 Jun 2020 09:54:53: 4000000 INFO @ Tue, 16 Jun 2020 09:54:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:55: #1 total tags in treatment: 9370942 INFO @ Tue, 16 Jun 2020 09:54:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:55: #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 09:54:55: #1 tags after filtering in treatment: 9370942 INFO @ Tue, 16 Jun 2020 09:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:56: #2 number of paired peaks: 302 WARNING @ Tue, 16 Jun 2020 09:54:56: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:56: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:54:56: #2 alternative fragment length(s) may be 4,47,595 bps INFO @ Tue, 16 Jun 2020 09:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:56: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:56: #2 You may need to consider one of the other alternative d(s): 4,47,595 WARNING @ Tue, 16 Jun 2020 09:54:56: #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 09:54:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:01: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:55:08: 6000000 INFO @ Tue, 16 Jun 2020 09:55:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:15: 7000000 INFO @ Tue, 16 Jun 2020 09:55:22: 8000000 INFO @ Tue, 16 Jun 2020 09:55:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.10_summits.bed INFO @ Tue, 16 Jun 2020 09:55:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (353 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:55:29: 9000000 INFO @ Tue, 16 Jun 2020 09:55:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:55:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:55:31: #1 total tags in treatment: 9370942 INFO @ Tue, 16 Jun 2020 09:55:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:31: #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 09:55:31: #1 tags after filtering in treatment: 9370942 INFO @ Tue, 16 Jun 2020 09:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:32: #2 number of paired peaks: 302 WARNING @ Tue, 16 Jun 2020 09:55:32: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:32: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:55:32: #2 alternative fragment length(s) may be 4,47,595 bps INFO @ Tue, 16 Jun 2020 09:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.20_model.r WARNING @ Tue, 16 Jun 2020 09:55:32: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:32: #2 You may need to consider one of the other alternative d(s): 4,47,595 WARNING @ Tue, 16 Jun 2020 09:55:32: #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 09:55:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982082/SRX982082.20_summits.bed INFO @ Tue, 16 Jun 2020 09:55:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (140 records, 4 fields): 1 millis CompletedMACS2peakCalling