Job ID = 6366763 SRX = SRX2228916 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:23 prefetch.2.10.7: 1) Downloading 'SRR4380372'... 2020-06-15T23:00:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:39 prefetch.2.10.7: 'SRR4380372' is valid 2020-06-15T23:01:39 prefetch.2.10.7: 1) 'SRR4380372' was downloaded successfully Read 11412023 spots for SRR4380372/SRR4380372.sra Written 11412023 spots for SRR4380372/SRR4380372.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: 00:03:42 11412023 reads; of these: 11412023 (100.00%) were unpaired; of these: 306686 (2.69%) aligned 0 times 9368074 (82.09%) aligned exactly 1 time 1737263 (15.22%) aligned >1 times 97.31% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 2913180 / 11105337 = 0.2623 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 08:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.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 08:09:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:54: 1000000 INFO @ Tue, 16 Jun 2020 08:10:01: 2000000 INFO @ Tue, 16 Jun 2020 08:10:08: 3000000 INFO @ Tue, 16 Jun 2020 08:10:14: 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 08:10:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.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 08:10:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:22: 5000000 INFO @ Tue, 16 Jun 2020 08:10:25: 1000000 INFO @ Tue, 16 Jun 2020 08:10:30: 6000000 INFO @ Tue, 16 Jun 2020 08:10:33: 2000000 INFO @ Tue, 16 Jun 2020 08:10:37: 7000000 INFO @ Tue, 16 Jun 2020 08:10:41: 3000000 INFO @ Tue, 16 Jun 2020 08:10:45: 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 08:10:47: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:10:47: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:10:47: #1 total tags in treatment: 8192157 INFO @ Tue, 16 Jun 2020 08:10:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:47: #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 08:10:47: #1 tags after filtering in treatment: 8192157 INFO @ Tue, 16 Jun 2020 08:10:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:47: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:10:47: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:47: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 08:10:47: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 16 Jun 2020 08:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.05_model.r WARNING @ Tue, 16 Jun 2020 08:10:47: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:47: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 16 Jun 2020 08:10:47: #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 08:10:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.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 08:10:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:49: 4000000 INFO @ Tue, 16 Jun 2020 08:10:57: 1000000 INFO @ Tue, 16 Jun 2020 08:10:58: 5000000 INFO @ Tue, 16 Jun 2020 08:11:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:07: 2000000 INFO @ Tue, 16 Jun 2020 08:11:07: 6000000 INFO @ Tue, 16 Jun 2020 08:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (523 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:16: 7000000 INFO @ Tue, 16 Jun 2020 08:11:16: 3000000 INFO @ Tue, 16 Jun 2020 08:11:24: 8000000 INFO @ Tue, 16 Jun 2020 08:11:26: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:11:26: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:11:26: #1 total tags in treatment: 8192157 INFO @ Tue, 16 Jun 2020 08:11:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:26: #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 08:11:26: 4000000 INFO @ Tue, 16 Jun 2020 08:11:26: #1 tags after filtering in treatment: 8192157 INFO @ Tue, 16 Jun 2020 08:11:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:27: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:11:27: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:27: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 08:11:27: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 16 Jun 2020 08:11:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.10_model.r WARNING @ Tue, 16 Jun 2020 08:11:27: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:27: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 16 Jun 2020 08:11:27: #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 08:11:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:35: 5000000 INFO @ Tue, 16 Jun 2020 08:11:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:43: 6000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:51: 7000000 INFO @ Tue, 16 Jun 2020 08:12:00: 8000000 INFO @ Tue, 16 Jun 2020 08:12:01: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:12:01: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:12:01: #1 total tags in treatment: 8192157 INFO @ Tue, 16 Jun 2020 08:12:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:01: #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 08:12:01: #1 tags after filtering in treatment: 8192157 INFO @ Tue, 16 Jun 2020 08:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:02: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:12:02: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:02: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 08:12:02: #2 alternative fragment length(s) may be 4,75 bps INFO @ Tue, 16 Jun 2020 08:12:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.20_model.r WARNING @ Tue, 16 Jun 2020 08:12:02: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:02: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Tue, 16 Jun 2020 08:12:02: #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 08:12:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228916/SRX2228916.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (216 records, 4 fields): 1 millis CompletedMACS2peakCalling