Job ID = 6507989 SRX = SRX657411 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:13:49 prefetch.2.10.7: 1) Downloading 'SRR1520420'... 2020-06-26T13:13:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:15:27 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:15:28 prefetch.2.10.7: 'SRR1520420' is valid 2020-06-26T13:15:28 prefetch.2.10.7: 1) 'SRR1520420' was downloaded successfully Read 13371138 spots for SRR1520420/SRR1520420.sra Written 13371138 spots for SRR1520420/SRR1520420.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: 00:02:15 13371138 reads; of these: 13371138 (100.00%) were unpaired; of these: 5205389 (38.93%) aligned 0 times 6785771 (50.75%) aligned exactly 1 time 1379978 (10.32%) aligned >1 times 61.07% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 1634618 / 8165749 = 0.2002 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 22:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.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 22:21:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:21:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:21:39: 1000000 INFO @ Fri, 26 Jun 2020 22:21:45: 2000000 INFO @ Fri, 26 Jun 2020 22:21:51: 3000000 INFO @ Fri, 26 Jun 2020 22:21:58: 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 22:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.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 22:22:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:22:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:22:04: 5000000 INFO @ Fri, 26 Jun 2020 22:22:11: 6000000 INFO @ Fri, 26 Jun 2020 22:22:11: 1000000 INFO @ Fri, 26 Jun 2020 22:22:14: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 22:22:14: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 22:22:14: #1 total tags in treatment: 6531131 INFO @ Fri, 26 Jun 2020 22:22:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:22:14: #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 22:22:15: #1 tags after filtering in treatment: 6531131 INFO @ Fri, 26 Jun 2020 22:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:22:15: #1 finished! INFO @ Fri, 26 Jun 2020 22:22:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:22:15: #2 number of paired peaks: 429 WARNING @ Fri, 26 Jun 2020 22:22:15: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Fri, 26 Jun 2020 22:22:15: start model_add_line... INFO @ Fri, 26 Jun 2020 22:22:15: start X-correlation... INFO @ Fri, 26 Jun 2020 22:22:15: end of X-cor INFO @ Fri, 26 Jun 2020 22:22:15: #2 finished! INFO @ Fri, 26 Jun 2020 22:22:15: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 22:22:15: #2 alternative fragment length(s) may be 4,53 bps INFO @ Fri, 26 Jun 2020 22:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.05_model.r WARNING @ Fri, 26 Jun 2020 22:22:15: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:22:15: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Fri, 26 Jun 2020 22:22:15: #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 22:22:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:22:20: 2000000 INFO @ Fri, 26 Jun 2020 22:22:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:22:29: 3000000 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 22:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.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 22:22:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:22:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:22:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.05_summits.bed INFO @ Fri, 26 Jun 2020 22:22:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (980 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:22:37: 4000000 INFO @ Fri, 26 Jun 2020 22:22:40: 1000000 INFO @ Fri, 26 Jun 2020 22:22:45: 5000000 INFO @ Fri, 26 Jun 2020 22:22:48: 2000000 INFO @ Fri, 26 Jun 2020 22:22:53: 6000000 INFO @ Fri, 26 Jun 2020 22:22:55: 3000000 INFO @ Fri, 26 Jun 2020 22:22:57: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 22:22:57: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 22:22:57: #1 total tags in treatment: 6531131 INFO @ Fri, 26 Jun 2020 22:22:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:22:57: #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 22:22:57: #1 tags after filtering in treatment: 6531131 INFO @ Fri, 26 Jun 2020 22:22:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:22:57: #1 finished! INFO @ Fri, 26 Jun 2020 22:22:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:22:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:22:58: #2 number of paired peaks: 429 WARNING @ Fri, 26 Jun 2020 22:22:58: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Fri, 26 Jun 2020 22:22:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:22:58: start X-correlation... INFO @ Fri, 26 Jun 2020 22:22:58: end of X-cor INFO @ Fri, 26 Jun 2020 22:22:58: #2 finished! INFO @ Fri, 26 Jun 2020 22:22:58: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 22:22:58: #2 alternative fragment length(s) may be 4,53 bps INFO @ Fri, 26 Jun 2020 22:22:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.10_model.r WARNING @ Fri, 26 Jun 2020 22:22:58: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:22:58: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Fri, 26 Jun 2020 22:22:58: #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 22:22:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:22:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:23:04: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:23:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:23:12: 5000000 INFO @ Fri, 26 Jun 2020 22:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.10_summits.bed INFO @ Fri, 26 Jun 2020 22:23:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:23:19: 6000000 INFO @ Fri, 26 Jun 2020 22:23:24: #1 tag size is determined as 46 bps INFO @ Fri, 26 Jun 2020 22:23:24: #1 tag size = 46 INFO @ Fri, 26 Jun 2020 22:23:24: #1 total tags in treatment: 6531131 INFO @ Fri, 26 Jun 2020 22:23:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:23:24: #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 22:23:24: #1 tags after filtering in treatment: 6531131 INFO @ Fri, 26 Jun 2020 22:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:23:24: #1 finished! INFO @ Fri, 26 Jun 2020 22:23:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:23:24: #2 number of paired peaks: 429 WARNING @ Fri, 26 Jun 2020 22:23:24: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Fri, 26 Jun 2020 22:23:24: start model_add_line... INFO @ Fri, 26 Jun 2020 22:23:24: start X-correlation... INFO @ Fri, 26 Jun 2020 22:23:24: end of X-cor INFO @ Fri, 26 Jun 2020 22:23:24: #2 finished! INFO @ Fri, 26 Jun 2020 22:23:24: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 22:23:24: #2 alternative fragment length(s) may be 4,53 bps INFO @ Fri, 26 Jun 2020 22:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.20_model.r WARNING @ Fri, 26 Jun 2020 22:23:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:23:24: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Fri, 26 Jun 2020 22:23:24: #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 22:23:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:23:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:23:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX657411/SRX657411.20_summits.bed INFO @ Fri, 26 Jun 2020 22:23:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (196 records, 4 fields): 2 millis CompletedMACS2peakCalling