Job ID = 6369040 SRX = SRX982104 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:40 prefetch.2.10.7: 1) Downloading 'SRR1956591'... 2020-06-16T00:34:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:34 prefetch.2.10.7: 'SRR1956591' is valid 2020-06-16T00:35:34 prefetch.2.10.7: 1) 'SRR1956591' was downloaded successfully Read 6657936 spots for SRR1956591/SRR1956591.sra Written 6657936 spots for SRR1956591/SRR1956591.sra 2020-06-16T00:36:03 prefetch.2.10.7: 1) Downloading 'SRR1956592'... 2020-06-16T00:36:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:59 prefetch.2.10.7: 'SRR1956592' is valid 2020-06-16T00:36:59 prefetch.2.10.7: 1) 'SRR1956592' was downloaded successfully Read 7293418 spots for SRR1956592/SRR1956592.sra Written 7293418 spots for SRR1956592/SRR1956592.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: 00:02:58 13951354 reads; of these: 13951354 (100.00%) were unpaired; of these: 1664927 (11.93%) aligned 0 times 10195646 (73.08%) aligned exactly 1 time 2090781 (14.99%) aligned >1 times 88.07% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 918974 / 12286427 = 0.0748 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 09:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.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 09:44:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:36: 1000000 INFO @ Tue, 16 Jun 2020 09:44:43: 2000000 INFO @ Tue, 16 Jun 2020 09:44:50: 3000000 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 09:44:58: 4000000 INFO @ Tue, 16 Jun 2020 09:44:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.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 09:44:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:05: 5000000 INFO @ Tue, 16 Jun 2020 09:45:08: 1000000 INFO @ Tue, 16 Jun 2020 09:45:13: 6000000 INFO @ Tue, 16 Jun 2020 09:45:16: 2000000 INFO @ Tue, 16 Jun 2020 09:45:21: 7000000 INFO @ Tue, 16 Jun 2020 09:45:24: 3000000 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 09:45:29: 8000000 INFO @ Tue, 16 Jun 2020 09:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.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 09:45:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:32: 4000000 INFO @ Tue, 16 Jun 2020 09:45:37: 9000000 INFO @ Tue, 16 Jun 2020 09:45:38: 1000000 INFO @ Tue, 16 Jun 2020 09:45:41: 5000000 INFO @ Tue, 16 Jun 2020 09:45:45: 10000000 INFO @ Tue, 16 Jun 2020 09:45:46: 2000000 INFO @ Tue, 16 Jun 2020 09:45:49: 6000000 INFO @ Tue, 16 Jun 2020 09:45:53: 11000000 INFO @ Tue, 16 Jun 2020 09:45:55: 3000000 INFO @ Tue, 16 Jun 2020 09:45:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:45:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:45:56: #1 total tags in treatment: 11367453 INFO @ Tue, 16 Jun 2020 09:45:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:56: #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 09:45:56: #1 tags after filtering in treatment: 11367453 INFO @ Tue, 16 Jun 2020 09:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:57: #2 number of paired peaks: 307 WARNING @ Tue, 16 Jun 2020 09:45:57: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:57: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:45:57: #2 alternative fragment length(s) may be 2,46,557 bps INFO @ Tue, 16 Jun 2020 09:45:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.05_model.r WARNING @ Tue, 16 Jun 2020 09:45:57: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:57: #2 You may need to consider one of the other alternative d(s): 2,46,557 WARNING @ Tue, 16 Jun 2020 09:45:57: #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 09:45:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:58: 7000000 INFO @ Tue, 16 Jun 2020 09:46:03: 4000000 INFO @ Tue, 16 Jun 2020 09:46:05: 8000000 INFO @ Tue, 16 Jun 2020 09:46:11: 5000000 INFO @ Tue, 16 Jun 2020 09:46:13: 9000000 INFO @ Tue, 16 Jun 2020 09:46:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:18: 6000000 INFO @ Tue, 16 Jun 2020 09:46:20: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:46:26: 7000000 INFO @ Tue, 16 Jun 2020 09:46:28: 11000000 INFO @ Tue, 16 Jun 2020 09:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.05_summits.bed INFO @ Tue, 16 Jun 2020 09:46:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:46:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:46:31: #1 total tags in treatment: 11367453 INFO @ Tue, 16 Jun 2020 09:46:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:31: #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 09:46:31: #1 tags after filtering in treatment: 11367453 INFO @ Tue, 16 Jun 2020 09:46:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:31: #2 number of paired peaks: 307 WARNING @ Tue, 16 Jun 2020 09:46:31: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:32: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:46:32: #2 alternative fragment length(s) may be 2,46,557 bps INFO @ Tue, 16 Jun 2020 09:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.10_model.r WARNING @ Tue, 16 Jun 2020 09:46:32: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:32: #2 You may need to consider one of the other alternative d(s): 2,46,557 WARNING @ Tue, 16 Jun 2020 09:46:32: #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 09:46:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:33: 8000000 INFO @ Tue, 16 Jun 2020 09:46:40: 9000000 INFO @ Tue, 16 Jun 2020 09:46:48: 10000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:55: 11000000 INFO @ Tue, 16 Jun 2020 09:46:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:46:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:46:57: #1 total tags in treatment: 11367453 INFO @ Tue, 16 Jun 2020 09:46:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:57: #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 09:46:57: #1 tags after filtering in treatment: 11367453 INFO @ Tue, 16 Jun 2020 09:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:58: #2 number of paired peaks: 307 WARNING @ Tue, 16 Jun 2020 09:46:58: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:58: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:46:58: #2 alternative fragment length(s) may be 2,46,557 bps INFO @ Tue, 16 Jun 2020 09:46:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.20_model.r WARNING @ Tue, 16 Jun 2020 09:46:58: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:58: #2 You may need to consider one of the other alternative d(s): 2,46,557 WARNING @ Tue, 16 Jun 2020 09:46:58: #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 09:46:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982104/SRX982104.20_summits.bed INFO @ Tue, 16 Jun 2020 09:47:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling