Job ID = 6366746 SRX = SRX2228899 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:15 prefetch.2.10.7: 1) Downloading 'SRR4380355'... 2020-06-15T22:54:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:52 prefetch.2.10.7: 'SRR4380355' is valid 2020-06-15T22:54:52 prefetch.2.10.7: 1) 'SRR4380355' was downloaded successfully 2020-06-15T22:54:52 prefetch.2.10.7: 'SRR4380355' has 0 unresolved dependencies Read 8579542 spots for SRR4380355/SRR4380355.sra Written 8579542 spots for SRR4380355/SRR4380355.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: 00:02:07 8579542 reads; of these: 8579542 (100.00%) were unpaired; of these: 135445 (1.58%) aligned 0 times 7014164 (81.75%) aligned exactly 1 time 1429933 (16.67%) aligned >1 times 98.42% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 494609 / 8444097 = 0.0586 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 08:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.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 08:00:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:11: 1000000 INFO @ Tue, 16 Jun 2020 08:00:17: 2000000 INFO @ Tue, 16 Jun 2020 08:00:23: 3000000 INFO @ Tue, 16 Jun 2020 08:00:29: 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 08:00:35: 5000000 INFO @ Tue, 16 Jun 2020 08:00:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.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 08:00:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:42: 6000000 INFO @ Tue, 16 Jun 2020 08:00:42: 1000000 INFO @ Tue, 16 Jun 2020 08:00:48: 7000000 INFO @ Tue, 16 Jun 2020 08:00:49: 2000000 INFO @ Tue, 16 Jun 2020 08:00:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:00:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:00:55: #1 total tags in treatment: 7949488 INFO @ Tue, 16 Jun 2020 08:00:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:00:55: #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 08:00:55: #1 tags after filtering in treatment: 7949488 INFO @ Tue, 16 Jun 2020 08:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:00:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:00:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:00:55: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 08:00:55: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 08:00:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:00:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:00:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:00:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:00:55: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:00:55: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 08:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.05_model.r WARNING @ Tue, 16 Jun 2020 08:00:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:00:55: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 08:00:55: #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 08:00:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:00:56: 3000000 INFO @ Tue, 16 Jun 2020 08:01:02: 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 08:01:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.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 08:01:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:08: 5000000 INFO @ Tue, 16 Jun 2020 08:01:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:01:12: 1000000 INFO @ Tue, 16 Jun 2020 08:01:15: 6000000 INFO @ Tue, 16 Jun 2020 08:01:19: 2000000 INFO @ Tue, 16 Jun 2020 08:01:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.05_summits.bed INFO @ Tue, 16 Jun 2020 08:01:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:22: 7000000 INFO @ Tue, 16 Jun 2020 08:01:26: 3000000 INFO @ Tue, 16 Jun 2020 08:01:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:01:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:01:28: #1 total tags in treatment: 7949488 INFO @ Tue, 16 Jun 2020 08:01:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:28: #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 08:01:28: #1 tags after filtering in treatment: 7949488 INFO @ Tue, 16 Jun 2020 08:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:29: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 08:01:29: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:29: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:01:29: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 08:01:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.10_model.r WARNING @ Tue, 16 Jun 2020 08:01:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:01:29: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 08:01:29: #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 08:01:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:32: 4000000 INFO @ Tue, 16 Jun 2020 08:01:39: 5000000 INFO @ Tue, 16 Jun 2020 08:01:45: 6000000 INFO @ Tue, 16 Jun 2020 08:01:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:01:51: 7000000 INFO @ Tue, 16 Jun 2020 08:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.10_summits.bed INFO @ Tue, 16 Jun 2020 08:01:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (299 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:01:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:01:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:01:57: #1 total tags in treatment: 7949488 INFO @ Tue, 16 Jun 2020 08:01:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:57: #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 08:01:57: #1 tags after filtering in treatment: 7949488 INFO @ Tue, 16 Jun 2020 08:01:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:58: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 08:01:58: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:58: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:01:58: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 08:01:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.20_model.r WARNING @ Tue, 16 Jun 2020 08:01:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:01:58: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 08:01:58: #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 08:01:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:02:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228899/SRX2228899.20_summits.bed INFO @ Tue, 16 Jun 2020 08:02:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 1 millis CompletedMACS2peakCalling