Job ID = 6366823 SRX = SRX2350722 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:20 prefetch.2.10.7: 1) Downloading 'SRR5024031'... 2020-06-15T23:29:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:01 prefetch.2.10.7: 'SRR5024031' is valid 2020-06-15T23:32:01 prefetch.2.10.7: 1) 'SRR5024031' was downloaded successfully Read 9424627 spots for SRR5024031/SRR5024031.sra Written 9424627 spots for SRR5024031/SRR5024031.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: 00:00:01 Multiseed full-index search: 00:02:21 9424627 reads; of these: 9424627 (100.00%) were unpaired; of these: 107475 (1.14%) aligned 0 times 7006034 (74.34%) aligned exactly 1 time 2311118 (24.52%) aligned >1 times 98.86% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 1084710 / 9317152 = 0.1164 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 08:37:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.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 08:37:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:41: 1000000 INFO @ Tue, 16 Jun 2020 08:37:46: 2000000 INFO @ Tue, 16 Jun 2020 08:37:51: 3000000 INFO @ Tue, 16 Jun 2020 08:37:56: 4000000 INFO @ Tue, 16 Jun 2020 08:38:01: 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 @ Tue, 16 Jun 2020 08:38:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.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 08:38:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:07: 6000000 INFO @ Tue, 16 Jun 2020 08:38:11: 1000000 INFO @ Tue, 16 Jun 2020 08:38:13: 7000000 INFO @ Tue, 16 Jun 2020 08:38:18: 2000000 INFO @ Tue, 16 Jun 2020 08:38:19: 8000000 INFO @ Tue, 16 Jun 2020 08:38:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:38:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:38:20: #1 total tags in treatment: 8232442 INFO @ Tue, 16 Jun 2020 08:38:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:20: #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 08:38:20: #1 tags after filtering in treatment: 8232442 INFO @ Tue, 16 Jun 2020 08:38:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:21: #2 number of paired peaks: 691 WARNING @ Tue, 16 Jun 2020 08:38:21: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:21: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:38:21: #2 alternative fragment length(s) may be 3,58 bps INFO @ Tue, 16 Jun 2020 08:38:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.05_model.r WARNING @ Tue, 16 Jun 2020 08:38:21: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:38:21: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Tue, 16 Jun 2020 08:38:21: #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 08:38:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:38:24: 3000000 INFO @ Tue, 16 Jun 2020 08:38:29: 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 @ Tue, 16 Jun 2020 08:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.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 08:38:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:35: 5000000 INFO @ Tue, 16 Jun 2020 08:38:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:41: 6000000 INFO @ Tue, 16 Jun 2020 08:38:42: 1000000 INFO @ Tue, 16 Jun 2020 08:38:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.05_summits.bed INFO @ Tue, 16 Jun 2020 08:38:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (723 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:38:48: 7000000 INFO @ Tue, 16 Jun 2020 08:38:48: 2000000 INFO @ Tue, 16 Jun 2020 08:38:54: 8000000 INFO @ Tue, 16 Jun 2020 08:38:54: 3000000 INFO @ Tue, 16 Jun 2020 08:38:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:38:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:38:55: #1 total tags in treatment: 8232442 INFO @ Tue, 16 Jun 2020 08:38:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:55: #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 08:38:55: #1 tags after filtering in treatment: 8232442 INFO @ Tue, 16 Jun 2020 08:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:56: #2 number of paired peaks: 691 WARNING @ Tue, 16 Jun 2020 08:38:56: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:56: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:38:56: #2 alternative fragment length(s) may be 3,58 bps INFO @ Tue, 16 Jun 2020 08:38:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.10_model.r WARNING @ Tue, 16 Jun 2020 08:38:56: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:38:56: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Tue, 16 Jun 2020 08:38:56: #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 08:38:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:00: 4000000 INFO @ Tue, 16 Jun 2020 08:39:06: 5000000 INFO @ Tue, 16 Jun 2020 08:39:12: 6000000 INFO @ Tue, 16 Jun 2020 08:39:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:39:18: 7000000 INFO @ Tue, 16 Jun 2020 08:39:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.10_summits.bed INFO @ Tue, 16 Jun 2020 08:39:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (483 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:39:24: 8000000 INFO @ Tue, 16 Jun 2020 08:39:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:39:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:39:25: #1 total tags in treatment: 8232442 INFO @ Tue, 16 Jun 2020 08:39:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:25: #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 08:39:25: #1 tags after filtering in treatment: 8232442 INFO @ Tue, 16 Jun 2020 08:39:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:26: #2 number of paired peaks: 691 WARNING @ Tue, 16 Jun 2020 08:39:26: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:26: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:39:26: #2 alternative fragment length(s) may be 3,58 bps INFO @ Tue, 16 Jun 2020 08:39:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.20_model.r WARNING @ Tue, 16 Jun 2020 08:39:26: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:26: #2 You may need to consider one of the other alternative d(s): 3,58 WARNING @ Tue, 16 Jun 2020 08:39:26: #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 08:39:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:39:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350722/SRX2350722.20_summits.bed INFO @ Tue, 16 Jun 2020 08:39:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 1 millis CompletedMACS2peakCalling