Job ID = 6369024 SRX = SRX982089 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:37:46 prefetch.2.10.7: 1) Downloading 'SRR1956576'... 2020-06-16T00:37:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:41:55 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:41:55 prefetch.2.10.7: 1) 'SRR1956576' was downloaded successfully Read 14068260 spots for SRR1956576/SRR1956576.sra Written 14068260 spots for SRR1956576/SRR1956576.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: 00:04:24 14068260 reads; of these: 14068260 (100.00%) were unpaired; of these: 937580 (6.66%) aligned 0 times 10974867 (78.01%) aligned exactly 1 time 2155813 (15.32%) aligned >1 times 93.34% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 2318479 / 13130680 = 0.1766 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 09:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.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 09:51:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:45: 1000000 INFO @ Tue, 16 Jun 2020 09:51:51: 2000000 INFO @ Tue, 16 Jun 2020 09:51:58: 3000000 INFO @ Tue, 16 Jun 2020 09:52:04: 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 09:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.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 09:52:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:11: 5000000 INFO @ Tue, 16 Jun 2020 09:52:16: 1000000 INFO @ Tue, 16 Jun 2020 09:52:18: 6000000 INFO @ Tue, 16 Jun 2020 09:52:23: 2000000 INFO @ Tue, 16 Jun 2020 09:52:25: 7000000 INFO @ Tue, 16 Jun 2020 09:52:30: 3000000 INFO @ Tue, 16 Jun 2020 09:52:32: 8000000 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 09:52:37: 4000000 INFO @ Tue, 16 Jun 2020 09:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.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 09:52:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:39: 9000000 INFO @ Tue, 16 Jun 2020 09:52:44: 5000000 INFO @ Tue, 16 Jun 2020 09:52:45: 1000000 INFO @ Tue, 16 Jun 2020 09:52:47: 10000000 INFO @ Tue, 16 Jun 2020 09:52:51: 2000000 INFO @ Tue, 16 Jun 2020 09:52:51: 6000000 INFO @ Tue, 16 Jun 2020 09:52:52: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:52:52: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:52:52: #1 total tags in treatment: 10812201 INFO @ Tue, 16 Jun 2020 09:52:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:52: #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 09:52:53: #1 tags after filtering in treatment: 10812201 INFO @ Tue, 16 Jun 2020 09:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:53: #2 number of paired peaks: 342 WARNING @ Tue, 16 Jun 2020 09:52:53: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:53: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:52:53: #2 alternative fragment length(s) may be 4,72 bps INFO @ Tue, 16 Jun 2020 09:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.05_model.r WARNING @ Tue, 16 Jun 2020 09:52:53: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:53: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Tue, 16 Jun 2020 09:52:53: #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 09:52:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:57: 3000000 INFO @ Tue, 16 Jun 2020 09:52:59: 7000000 INFO @ Tue, 16 Jun 2020 09:53:03: 4000000 INFO @ Tue, 16 Jun 2020 09:53:06: 8000000 INFO @ Tue, 16 Jun 2020 09:53:09: 5000000 INFO @ Tue, 16 Jun 2020 09:53:13: 9000000 INFO @ Tue, 16 Jun 2020 09:53:15: 6000000 INFO @ Tue, 16 Jun 2020 09:53:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:20: 10000000 INFO @ Tue, 16 Jun 2020 09:53:21: 7000000 INFO @ Tue, 16 Jun 2020 09:53:25: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:53:25: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:53:25: #1 total tags in treatment: 10812201 INFO @ Tue, 16 Jun 2020 09:53:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:25: #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 09:53:26: #1 tags after filtering in treatment: 10812201 INFO @ Tue, 16 Jun 2020 09:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:26: #2 number of paired peaks: 342 WARNING @ Tue, 16 Jun 2020 09:53:26: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:26: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:53:26: #2 alternative fragment length(s) may be 4,72 bps INFO @ Tue, 16 Jun 2020 09:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.10_model.r INFO @ Tue, 16 Jun 2020 09:53:26: Done! WARNING @ Tue, 16 Jun 2020 09:53:26: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:26: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Tue, 16 Jun 2020 09:53:26: #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 09:53:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:26: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (558 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:27: 8000000 INFO @ Tue, 16 Jun 2020 09:53:33: 9000000 INFO @ Tue, 16 Jun 2020 09:53:39: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:53:44: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:53:44: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:53:44: #1 total tags in treatment: 10812201 INFO @ Tue, 16 Jun 2020 09:53:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:44: #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 09:53:44: #1 tags after filtering in treatment: 10812201 INFO @ Tue, 16 Jun 2020 09:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:45: #2 number of paired peaks: 342 WARNING @ Tue, 16 Jun 2020 09:53:45: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:45: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:53:45: #2 alternative fragment length(s) may be 4,72 bps INFO @ Tue, 16 Jun 2020 09:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.20_model.r WARNING @ Tue, 16 Jun 2020 09:53:45: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:45: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Tue, 16 Jun 2020 09:53:45: #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 09:53:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (394 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982089/SRX982089.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 1 millis CompletedMACS2peakCalling