Job ID = 6507814 SRX = SRX494819 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:44:46 prefetch.2.10.7: 1) Downloading 'SRR1198351'... 2020-06-26T13:44:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:45:48 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:45:48 prefetch.2.10.7: 'SRR1198351' is valid 2020-06-26T13:45:48 prefetch.2.10.7: 1) 'SRR1198351' was downloaded successfully Read 9807251 spots for SRR1198351/SRR1198351.sra Written 9807251 spots for SRR1198351/SRR1198351.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: 00:01:49 9807251 reads; of these: 9807251 (100.00%) were unpaired; of these: 293436 (2.99%) aligned 0 times 7730150 (78.82%) aligned exactly 1 time 1783665 (18.19%) aligned >1 times 97.01% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 784406 / 9513815 = 0.0824 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 22:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.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 22:51:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:51:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:51:17: 1000000 INFO @ Fri, 26 Jun 2020 22:51:22: 2000000 INFO @ Fri, 26 Jun 2020 22:51:27: 3000000 INFO @ Fri, 26 Jun 2020 22:51:32: 4000000 INFO @ Fri, 26 Jun 2020 22:51:37: 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 @ Fri, 26 Jun 2020 22:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.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 22:51:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:51:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:51:43: 6000000 INFO @ Fri, 26 Jun 2020 22:51:46: 1000000 INFO @ Fri, 26 Jun 2020 22:51:48: 7000000 INFO @ Fri, 26 Jun 2020 22:51:51: 2000000 INFO @ Fri, 26 Jun 2020 22:51:53: 8000000 INFO @ Fri, 26 Jun 2020 22:51:57: 3000000 INFO @ Fri, 26 Jun 2020 22:51:57: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:51:57: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:51:57: #1 total tags in treatment: 8729409 INFO @ Fri, 26 Jun 2020 22:51:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:51:57: #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 22:51:57: #1 tags after filtering in treatment: 8729409 INFO @ Fri, 26 Jun 2020 22:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:51:57: #1 finished! INFO @ Fri, 26 Jun 2020 22:51:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:51:58: #2 number of paired peaks: 342 WARNING @ Fri, 26 Jun 2020 22:51:58: 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 @ Fri, 26 Jun 2020 22:51:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:51:58: start X-correlation... INFO @ Fri, 26 Jun 2020 22:51:58: end of X-cor INFO @ Fri, 26 Jun 2020 22:51:58: #2 finished! INFO @ Fri, 26 Jun 2020 22:51:58: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 22:51:58: #2 alternative fragment length(s) may be 3,36,555 bps INFO @ Fri, 26 Jun 2020 22:51:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.05_model.r WARNING @ Fri, 26 Jun 2020 22:51:58: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:51:58: #2 You may need to consider one of the other alternative d(s): 3,36,555 WARNING @ Fri, 26 Jun 2020 22:51:58: #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 22:51:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:51:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:52:02: 4000000 INFO @ Fri, 26 Jun 2020 22:52:07: 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 @ Fri, 26 Jun 2020 22:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.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 22:52:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:52:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:52:12: 6000000 INFO @ Fri, 26 Jun 2020 22:52:16: 1000000 INFO @ Fri, 26 Jun 2020 22:52:18: 7000000 INFO @ Fri, 26 Jun 2020 22:52:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:52:22: 2000000 INFO @ Fri, 26 Jun 2020 22:52:23: 8000000 INFO @ Fri, 26 Jun 2020 22:52:27: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:52:27: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:52:27: #1 total tags in treatment: 8729409 INFO @ Fri, 26 Jun 2020 22:52:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:52:27: #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 22:52:27: #1 tags after filtering in treatment: 8729409 INFO @ Fri, 26 Jun 2020 22:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:52:27: #1 finished! INFO @ Fri, 26 Jun 2020 22:52:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:52:28: #2 number of paired peaks: 342 WARNING @ Fri, 26 Jun 2020 22:52:28: 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 @ Fri, 26 Jun 2020 22:52:28: start model_add_line... INFO @ Fri, 26 Jun 2020 22:52:28: 3000000 INFO @ Fri, 26 Jun 2020 22:52:28: start X-correlation... INFO @ Fri, 26 Jun 2020 22:52:28: end of X-cor INFO @ Fri, 26 Jun 2020 22:52:28: #2 finished! INFO @ Fri, 26 Jun 2020 22:52:28: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 22:52:28: #2 alternative fragment length(s) may be 3,36,555 bps INFO @ Fri, 26 Jun 2020 22:52:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.10_model.r WARNING @ Fri, 26 Jun 2020 22:52:28: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:52:28: #2 You may need to consider one of the other alternative d(s): 3,36,555 WARNING @ Fri, 26 Jun 2020 22:52:28: #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 22:52:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:52:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:52:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:52:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:52:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.05_summits.bed INFO @ Fri, 26 Jun 2020 22:52:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1208 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:52:34: 4000000 INFO @ Fri, 26 Jun 2020 22:52:40: 5000000 INFO @ Fri, 26 Jun 2020 22:52:45: 6000000 INFO @ Fri, 26 Jun 2020 22:52:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:52:51: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:52:57: 8000000 INFO @ Fri, 26 Jun 2020 22:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.10_summits.bed INFO @ Fri, 26 Jun 2020 22:52:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:53:01: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:53:01: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:53:01: #1 total tags in treatment: 8729409 INFO @ Fri, 26 Jun 2020 22:53:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:53:01: #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 22:53:01: #1 tags after filtering in treatment: 8729409 INFO @ Fri, 26 Jun 2020 22:53:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:53:01: #1 finished! INFO @ Fri, 26 Jun 2020 22:53:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:53:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:53:02: #2 number of paired peaks: 342 WARNING @ Fri, 26 Jun 2020 22:53:02: 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 @ Fri, 26 Jun 2020 22:53:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:53:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:53:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:53:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:53:02: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 22:53:02: #2 alternative fragment length(s) may be 3,36,555 bps INFO @ Fri, 26 Jun 2020 22:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.20_model.r WARNING @ Fri, 26 Jun 2020 22:53:02: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:53:02: #2 You may need to consider one of the other alternative d(s): 3,36,555 WARNING @ Fri, 26 Jun 2020 22:53:02: #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 22:53:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:53:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:53:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494819/SRX494819.20_summits.bed INFO @ Fri, 26 Jun 2020 22:53:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 millis CompletedMACS2peakCalling