Job ID = 6507939 SRX = SRX495101 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:12:18 prefetch.2.10.7: 1) Downloading 'SRR1198633'... 2020-06-26T13:12:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:15:46 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:15:46 prefetch.2.10.7: 1) 'SRR1198633' was downloaded successfully Read 16047878 spots for SRR1198633/SRR1198633.sra Written 16047878 spots for SRR1198633/SRR1198633.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: 00:02:58 16047878 reads; of these: 16047878 (100.00%) were unpaired; of these: 1451139 (9.04%) aligned 0 times 12366263 (77.06%) aligned exactly 1 time 2230476 (13.90%) aligned >1 times 90.96% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 1646664 / 14596739 = 0.1128 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 @ Fri, 26 Jun 2020 22:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.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 @ Fri, 26 Jun 2020 22:24:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:24:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:24:12: 1000000 INFO @ Fri, 26 Jun 2020 22:24:18: 2000000 INFO @ Fri, 26 Jun 2020 22:24:24: 3000000 INFO @ Fri, 26 Jun 2020 22:24:30: 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 @ Fri, 26 Jun 2020 22:24:35: 5000000 INFO @ Fri, 26 Jun 2020 22:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.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 @ Fri, 26 Jun 2020 22:24:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:24:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:24:41: 6000000 INFO @ Fri, 26 Jun 2020 22:24:42: 1000000 INFO @ Fri, 26 Jun 2020 22:24:47: 7000000 INFO @ Fri, 26 Jun 2020 22:24:48: 2000000 INFO @ Fri, 26 Jun 2020 22:24:53: 8000000 INFO @ Fri, 26 Jun 2020 22:24:54: 3000000 INFO @ Fri, 26 Jun 2020 22:25:00: 9000000 INFO @ Fri, 26 Jun 2020 22:25:00: 4000000 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 @ Fri, 26 Jun 2020 22:25:06: 5000000 INFO @ Fri, 26 Jun 2020 22:25:06: 10000000 INFO @ Fri, 26 Jun 2020 22:25:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.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 @ Fri, 26 Jun 2020 22:25:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:25:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:25:12: 6000000 INFO @ Fri, 26 Jun 2020 22:25:13: 11000000 INFO @ Fri, 26 Jun 2020 22:25:13: 1000000 INFO @ Fri, 26 Jun 2020 22:25:18: 7000000 INFO @ Fri, 26 Jun 2020 22:25:19: 12000000 INFO @ Fri, 26 Jun 2020 22:25:20: 2000000 INFO @ Fri, 26 Jun 2020 22:25:24: 8000000 INFO @ Fri, 26 Jun 2020 22:25:26: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:25:26: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:25:26: #1 total tags in treatment: 12950075 INFO @ Fri, 26 Jun 2020 22:25:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:25:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:25:26: #1 tags after filtering in treatment: 12950075 INFO @ Fri, 26 Jun 2020 22:25:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:25:26: #1 finished! INFO @ Fri, 26 Jun 2020 22:25:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:25:27: 3000000 INFO @ Fri, 26 Jun 2020 22:25:27: #2 number of paired peaks: 268 WARNING @ Fri, 26 Jun 2020 22:25:27: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Fri, 26 Jun 2020 22:25:27: start model_add_line... INFO @ Fri, 26 Jun 2020 22:25:27: start X-correlation... INFO @ Fri, 26 Jun 2020 22:25:27: end of X-cor INFO @ Fri, 26 Jun 2020 22:25:27: #2 finished! INFO @ Fri, 26 Jun 2020 22:25:27: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:25:27: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.05_model.r WARNING @ Fri, 26 Jun 2020 22:25:27: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:25:27: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:25:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:25:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:25:30: 9000000 INFO @ Fri, 26 Jun 2020 22:25:33: 4000000 INFO @ Fri, 26 Jun 2020 22:25:36: 10000000 INFO @ Fri, 26 Jun 2020 22:25:39: 5000000 INFO @ Fri, 26 Jun 2020 22:25:42: 11000000 INFO @ Fri, 26 Jun 2020 22:25:46: 6000000 INFO @ Fri, 26 Jun 2020 22:25:48: 12000000 INFO @ Fri, 26 Jun 2020 22:25:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:25:52: 7000000 INFO @ Fri, 26 Jun 2020 22:25:53: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:25:53: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:25:53: #1 total tags in treatment: 12950075 INFO @ Fri, 26 Jun 2020 22:25:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:25:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:25:53: #1 tags after filtering in treatment: 12950075 INFO @ Fri, 26 Jun 2020 22:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:25:53: #1 finished! INFO @ Fri, 26 Jun 2020 22:25:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:25:54: #2 number of paired peaks: 268 WARNING @ Fri, 26 Jun 2020 22:25:54: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Fri, 26 Jun 2020 22:25:54: start model_add_line... INFO @ Fri, 26 Jun 2020 22:25:54: start X-correlation... INFO @ Fri, 26 Jun 2020 22:25:54: end of X-cor INFO @ Fri, 26 Jun 2020 22:25:54: #2 finished! INFO @ Fri, 26 Jun 2020 22:25:54: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:25:54: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:25:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.10_model.r WARNING @ Fri, 26 Jun 2020 22:25:54: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:25:54: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:25:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:25:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:25:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:25:58: 8000000 INFO @ Fri, 26 Jun 2020 22:26:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:26:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.05_summits.bed INFO @ Fri, 26 Jun 2020 22:26:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:26:04: 9000000 INFO @ Fri, 26 Jun 2020 22:26:10: 10000000 INFO @ Fri, 26 Jun 2020 22:26:16: 11000000 INFO @ Fri, 26 Jun 2020 22:26:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:26:22: 12000000 INFO @ Fri, 26 Jun 2020 22:26:27: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:26:27: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:26:27: #1 total tags in treatment: 12950075 INFO @ Fri, 26 Jun 2020 22:26:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:26:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:26:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:26:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:26:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.10_summits.bed INFO @ Fri, 26 Jun 2020 22:26:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (361 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:26:28: #1 tags after filtering in treatment: 12950075 INFO @ Fri, 26 Jun 2020 22:26:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:26:28: #1 finished! INFO @ Fri, 26 Jun 2020 22:26:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:26:28: #2 number of paired peaks: 268 WARNING @ Fri, 26 Jun 2020 22:26:28: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Fri, 26 Jun 2020 22:26:28: start model_add_line... INFO @ Fri, 26 Jun 2020 22:26:28: start X-correlation... INFO @ Fri, 26 Jun 2020 22:26:29: end of X-cor INFO @ Fri, 26 Jun 2020 22:26:29: #2 finished! INFO @ Fri, 26 Jun 2020 22:26:29: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:26:29: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.20_model.r WARNING @ Fri, 26 Jun 2020 22:26:29: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:26:29: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:26:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:26:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:26:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:26:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:27:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:27:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:27:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495101/SRX495101.20_summits.bed INFO @ Fri, 26 Jun 2020 22:27:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (126 records, 4 fields): 2 millis CompletedMACS2peakCalling