Job ID = 6367255 SRX = SRX323676 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:22:16 prefetch.2.10.7: 1) Downloading 'SRR935764'... 2020-06-15T23:22:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:41 prefetch.2.10.7: 'SRR935764' is valid 2020-06-15T23:23:41 prefetch.2.10.7: 1) 'SRR935764' was downloaded successfully Read 13737468 spots for SRR935764/SRR935764.sra Written 13737468 spots for SRR935764/SRR935764.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: 00:03:38 13737468 reads; of these: 13737468 (100.00%) were unpaired; of these: 1419444 (10.33%) aligned 0 times 10616140 (77.28%) aligned exactly 1 time 1701884 (12.39%) aligned >1 times 89.67% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 3210661 / 12318024 = 0.2606 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 08:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.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 08:31:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:54: 1000000 INFO @ Tue, 16 Jun 2020 08:32:00: 2000000 INFO @ Tue, 16 Jun 2020 08:32:05: 3000000 INFO @ Tue, 16 Jun 2020 08:32:11: 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 08:32:17: 5000000 INFO @ Tue, 16 Jun 2020 08:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.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 08:32:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:24: 6000000 INFO @ Tue, 16 Jun 2020 08:32:24: 1000000 INFO @ Tue, 16 Jun 2020 08:32:30: 7000000 INFO @ Tue, 16 Jun 2020 08:32:30: 2000000 INFO @ Tue, 16 Jun 2020 08:32:36: 8000000 INFO @ Tue, 16 Jun 2020 08:32:37: 3000000 INFO @ Tue, 16 Jun 2020 08:32:43: 9000000 INFO @ Tue, 16 Jun 2020 08:32:43: 4000000 INFO @ Tue, 16 Jun 2020 08:32:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:32:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:32:43: #1 total tags in treatment: 9107363 INFO @ Tue, 16 Jun 2020 08:32:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:43: #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 08:32:43: #1 tags after filtering in treatment: 9107363 INFO @ Tue, 16 Jun 2020 08:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:44: #2 number of paired peaks: 104 WARNING @ Tue, 16 Jun 2020 08:32:44: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:44: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:32:44: #2 alternative fragment length(s) may be 50,98,115,197,322,427,432,571,576 bps INFO @ Tue, 16 Jun 2020 08:32:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.05_model.r WARNING @ Tue, 16 Jun 2020 08:32:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:44: #2 You may need to consider one of the other alternative d(s): 50,98,115,197,322,427,432,571,576 WARNING @ Tue, 16 Jun 2020 08:32:44: #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 08:32:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:44: #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 08:32:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.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 08:32:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:49: 5000000 INFO @ Tue, 16 Jun 2020 08:32:55: 1000000 INFO @ Tue, 16 Jun 2020 08:32:56: 6000000 INFO @ Tue, 16 Jun 2020 08:33:01: 2000000 INFO @ Tue, 16 Jun 2020 08:33:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:03: 7000000 INFO @ Tue, 16 Jun 2020 08:33:08: 3000000 INFO @ Tue, 16 Jun 2020 08:33:10: 8000000 INFO @ Tue, 16 Jun 2020 08:33:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:14: 4000000 INFO @ Tue, 16 Jun 2020 08:33:16: 9000000 INFO @ Tue, 16 Jun 2020 08:33:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:17: #1 total tags in treatment: 9107363 INFO @ Tue, 16 Jun 2020 08:33:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:17: #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 08:33:17: #1 tags after filtering in treatment: 9107363 INFO @ Tue, 16 Jun 2020 08:33:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:18: #2 number of paired peaks: 104 WARNING @ Tue, 16 Jun 2020 08:33:18: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:18: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:33:18: #2 alternative fragment length(s) may be 50,98,115,197,322,427,432,571,576 bps INFO @ Tue, 16 Jun 2020 08:33:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.10_model.r WARNING @ Tue, 16 Jun 2020 08:33:18: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:18: #2 You may need to consider one of the other alternative d(s): 50,98,115,197,322,427,432,571,576 WARNING @ Tue, 16 Jun 2020 08:33:18: #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 08:33:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:21: 5000000 INFO @ Tue, 16 Jun 2020 08:33:27: 6000000 INFO @ Tue, 16 Jun 2020 08:33:33: 7000000 INFO @ Tue, 16 Jun 2020 08:33:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:39: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (98 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:45: 9000000 INFO @ Tue, 16 Jun 2020 08:33:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:45: #1 total tags in treatment: 9107363 INFO @ Tue, 16 Jun 2020 08:33:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:45: #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 08:33:46: #1 tags after filtering in treatment: 9107363 INFO @ Tue, 16 Jun 2020 08:33:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:46: #2 number of paired peaks: 104 WARNING @ Tue, 16 Jun 2020 08:33:46: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:46: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:33:46: #2 alternative fragment length(s) may be 50,98,115,197,322,427,432,571,576 bps INFO @ Tue, 16 Jun 2020 08:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.20_model.r WARNING @ Tue, 16 Jun 2020 08:33:46: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:46: #2 You may need to consider one of the other alternative d(s): 50,98,115,197,322,427,432,571,576 WARNING @ Tue, 16 Jun 2020 08:33:46: #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 08:33:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX323676/SRX323676.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling