Job ID = 6367671 SRX = SRX3862410 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:45:14 prefetch.2.10.7: 1) Downloading 'SRR6914646'... 2020-06-15T23:45:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:49 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:50 prefetch.2.10.7: 'SRR6914646' is valid 2020-06-15T23:47:50 prefetch.2.10.7: 1) 'SRR6914646' was downloaded successfully 2020-06-15T23:47:50 prefetch.2.10.7: 'SRR6914646' has 0 unresolved dependencies Read 14096832 spots for SRR6914646/SRR6914646.sra Written 14096832 spots for SRR6914646/SRR6914646.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: 00:04:18 14096832 reads; of these: 14096832 (100.00%) were unpaired; of these: 4418571 (31.34%) aligned 0 times 7949672 (56.39%) aligned exactly 1 time 1728589 (12.26%) aligned >1 times 68.66% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 1011046 / 9678261 = 0.1045 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 08:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.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 08:56:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:21: 1000000 INFO @ Tue, 16 Jun 2020 08:56:27: 2000000 INFO @ Tue, 16 Jun 2020 08:56:34: 3000000 INFO @ Tue, 16 Jun 2020 08:56:40: 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 08:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.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 08:56:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:47: 5000000 INFO @ Tue, 16 Jun 2020 08:56:52: 1000000 INFO @ Tue, 16 Jun 2020 08:56:54: 6000000 INFO @ Tue, 16 Jun 2020 08:56:59: 2000000 INFO @ Tue, 16 Jun 2020 08:57:01: 7000000 INFO @ Tue, 16 Jun 2020 08:57:06: 3000000 INFO @ Tue, 16 Jun 2020 08:57:08: 8000000 INFO @ Tue, 16 Jun 2020 08:57:12: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:57:12: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:57:12: #1 total tags in treatment: 8667215 INFO @ Tue, 16 Jun 2020 08:57:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:12: #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 08:57:12: #1 tags after filtering in treatment: 8667215 INFO @ Tue, 16 Jun 2020 08:57:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:12: #2 looking for paired plus/minus strand peaks... 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 08:57:13: 4000000 INFO @ Tue, 16 Jun 2020 08:57:13: #2 number of paired peaks: 300 WARNING @ Tue, 16 Jun 2020 08:57:13: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:13: #2 predicted fragment length is 65 bps INFO @ Tue, 16 Jun 2020 08:57:13: #2 alternative fragment length(s) may be 4,65 bps INFO @ Tue, 16 Jun 2020 08:57:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.05_model.r WARNING @ Tue, 16 Jun 2020 08:57:13: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:13: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Tue, 16 Jun 2020 08:57:13: #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 08:57:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.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 08:57:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:20: 5000000 INFO @ Tue, 16 Jun 2020 08:57:22: 1000000 INFO @ Tue, 16 Jun 2020 08:57:27: 6000000 INFO @ Tue, 16 Jun 2020 08:57:29: 2000000 INFO @ Tue, 16 Jun 2020 08:57:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:34: 7000000 INFO @ Tue, 16 Jun 2020 08:57:36: 3000000 INFO @ Tue, 16 Jun 2020 08:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (467 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:42: 8000000 INFO @ Tue, 16 Jun 2020 08:57:43: 4000000 INFO @ Tue, 16 Jun 2020 08:57:47: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:57:47: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:57:47: #1 total tags in treatment: 8667215 INFO @ Tue, 16 Jun 2020 08:57:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:47: #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 08:57:47: #1 tags after filtering in treatment: 8667215 INFO @ Tue, 16 Jun 2020 08:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:48: #2 number of paired peaks: 300 WARNING @ Tue, 16 Jun 2020 08:57:48: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:48: #2 predicted fragment length is 65 bps INFO @ Tue, 16 Jun 2020 08:57:48: #2 alternative fragment length(s) may be 4,65 bps INFO @ Tue, 16 Jun 2020 08:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.10_model.r WARNING @ Tue, 16 Jun 2020 08:57:48: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:48: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Tue, 16 Jun 2020 08:57:48: #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 08:57:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:51: 5000000 INFO @ Tue, 16 Jun 2020 08:57:57: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:58:04: 7000000 INFO @ Tue, 16 Jun 2020 08:58:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:11: 8000000 INFO @ Tue, 16 Jun 2020 08:58:15: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:58:15: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:58:15: #1 total tags in treatment: 8667215 INFO @ Tue, 16 Jun 2020 08:58:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:15: #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 08:58:15: #1 tags after filtering in treatment: 8667215 INFO @ Tue, 16 Jun 2020 08:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (332 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:16: #2 number of paired peaks: 300 WARNING @ Tue, 16 Jun 2020 08:58:16: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:16: #2 predicted fragment length is 65 bps INFO @ Tue, 16 Jun 2020 08:58:16: #2 alternative fragment length(s) may be 4,65 bps INFO @ Tue, 16 Jun 2020 08:58:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.20_model.r WARNING @ Tue, 16 Jun 2020 08:58:16: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:58:16: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Tue, 16 Jun 2020 08:58:16: #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 08:58:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:58:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862410/SRX3862410.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (183 records, 4 fields): 1 millis CompletedMACS2peakCalling