Job ID = 6367368 SRX = SRX331127 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:20 prefetch.2.10.7: 1) Downloading 'SRR947358'... 2020-06-15T23:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:54 prefetch.2.10.7: 'SRR947358' is valid 2020-06-15T23:35:54 prefetch.2.10.7: 1) 'SRR947358' was downloaded successfully Read 9219334 spots for SRR947358/SRR947358.sra Written 9219334 spots for SRR947358/SRR947358.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: 00:01:14 9219334 reads; of these: 9219334 (100.00%) were unpaired; of these: 3554622 (38.56%) aligned 0 times 4817646 (52.26%) aligned exactly 1 time 847066 (9.19%) aligned >1 times 61.44% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 495459 / 5664712 = 0.0875 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 08:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.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 08:39:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:25: 1000000 INFO @ Tue, 16 Jun 2020 08:39:31: 2000000 INFO @ Tue, 16 Jun 2020 08:39:37: 3000000 INFO @ Tue, 16 Jun 2020 08:39:44: 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 08:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.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 08:39:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:50: 5000000 INFO @ Tue, 16 Jun 2020 08:39:51: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:39:51: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:39:51: #1 total tags in treatment: 5169253 INFO @ Tue, 16 Jun 2020 08:39:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:51: #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 08:39:51: #1 tags after filtering in treatment: 5169253 INFO @ Tue, 16 Jun 2020 08:39:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:52: #2 number of paired peaks: 395 WARNING @ Tue, 16 Jun 2020 08:39:52: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:52: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:39:52: #2 alternative fragment length(s) may be 3,32,439,505,549,567,596 bps INFO @ Tue, 16 Jun 2020 08:39:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.05_model.r WARNING @ Tue, 16 Jun 2020 08:39:52: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:52: #2 You may need to consider one of the other alternative d(s): 3,32,439,505,549,567,596 WARNING @ Tue, 16 Jun 2020 08:39:52: #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 08:39:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:55: 1000000 INFO @ Tue, 16 Jun 2020 08:40:01: 2000000 INFO @ Tue, 16 Jun 2020 08:40:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:08: 3000000 INFO @ Tue, 16 Jun 2020 08:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:14: 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 08:40:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.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 08:40:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:20: 5000000 INFO @ Tue, 16 Jun 2020 08:40:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:21: #1 total tags in treatment: 5169253 INFO @ Tue, 16 Jun 2020 08:40:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:21: #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 08:40:21: #1 tags after filtering in treatment: 5169253 INFO @ Tue, 16 Jun 2020 08:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:22: #2 number of paired peaks: 395 WARNING @ Tue, 16 Jun 2020 08:40:22: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:22: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:40:22: #2 alternative fragment length(s) may be 3,32,439,505,549,567,596 bps INFO @ Tue, 16 Jun 2020 08:40:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.10_model.r WARNING @ Tue, 16 Jun 2020 08:40:22: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:22: #2 You may need to consider one of the other alternative d(s): 3,32,439,505,549,567,596 WARNING @ Tue, 16 Jun 2020 08:40:22: #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 08:40:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:25: 1000000 INFO @ Tue, 16 Jun 2020 08:40:32: 2000000 INFO @ Tue, 16 Jun 2020 08:40:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:38: 3000000 INFO @ Tue, 16 Jun 2020 08:40:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.10_summits.bed INFO @ Tue, 16 Jun 2020 08:40:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:45: 4000000 INFO @ Tue, 16 Jun 2020 08:40:52: 5000000 INFO @ Tue, 16 Jun 2020 08:40:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:53: #1 total tags in treatment: 5169253 INFO @ Tue, 16 Jun 2020 08:40:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:53: #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 08:40:53: #1 tags after filtering in treatment: 5169253 INFO @ Tue, 16 Jun 2020 08:40:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:53: #2 number of paired peaks: 395 WARNING @ Tue, 16 Jun 2020 08:40:53: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:53: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:40:53: #2 alternative fragment length(s) may be 3,32,439,505,549,567,596 bps INFO @ Tue, 16 Jun 2020 08:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.20_model.r WARNING @ Tue, 16 Jun 2020 08:40:53: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:53: #2 You may need to consider one of the other alternative d(s): 3,32,439,505,549,567,596 WARNING @ Tue, 16 Jun 2020 08:40:53: #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 08:40:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331127/SRX331127.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 1 millis CompletedMACS2peakCalling