Job ID = 6369022 SRX = SRX982087 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:45:09 prefetch.2.10.7: 1) Downloading 'SRR1956574'... 2020-06-16T00:45:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:47:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:47:53 prefetch.2.10.7: 'SRR1956574' is valid 2020-06-16T00:47:53 prefetch.2.10.7: 1) 'SRR1956574' was downloaded successfully Read 19049026 spots for SRR1956574/SRR1956574.sra Written 19049026 spots for SRR1956574/SRR1956574.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: 00:03:21 19049026 reads; of these: 19049026 (100.00%) were unpaired; of these: 5770567 (30.29%) aligned 0 times 11035055 (57.93%) aligned exactly 1 time 2243404 (11.78%) aligned >1 times 69.71% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 942744 / 13278459 = 0.0710 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 09:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.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 09:55:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:54: 1000000 INFO @ Tue, 16 Jun 2020 09:56:00: 2000000 INFO @ Tue, 16 Jun 2020 09:56:07: 3000000 INFO @ Tue, 16 Jun 2020 09:56:13: 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 09:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.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 09:56:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:19: 5000000 INFO @ Tue, 16 Jun 2020 09:56:24: 1000000 INFO @ Tue, 16 Jun 2020 09:56:26: 6000000 INFO @ Tue, 16 Jun 2020 09:56:30: 2000000 INFO @ Tue, 16 Jun 2020 09:56:32: 7000000 INFO @ Tue, 16 Jun 2020 09:56:36: 3000000 INFO @ Tue, 16 Jun 2020 09:56:39: 8000000 INFO @ Tue, 16 Jun 2020 09:56:43: 4000000 INFO @ Tue, 16 Jun 2020 09:56:45: 9000000 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 09:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.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 09:56:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:49: 5000000 INFO @ Tue, 16 Jun 2020 09:56:51: 10000000 INFO @ Tue, 16 Jun 2020 09:56:54: 1000000 INFO @ Tue, 16 Jun 2020 09:56:55: 6000000 INFO @ Tue, 16 Jun 2020 09:56:58: 11000000 INFO @ Tue, 16 Jun 2020 09:57:00: 2000000 INFO @ Tue, 16 Jun 2020 09:57:01: 7000000 INFO @ Tue, 16 Jun 2020 09:57:05: 12000000 INFO @ Tue, 16 Jun 2020 09:57:06: 3000000 INFO @ Tue, 16 Jun 2020 09:57:07: 8000000 INFO @ Tue, 16 Jun 2020 09:57:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:57:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:57:07: #1 total tags in treatment: 12335715 INFO @ Tue, 16 Jun 2020 09:57:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:07: #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 09:57:07: #1 tags after filtering in treatment: 12335715 INFO @ Tue, 16 Jun 2020 09:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:08: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 09:57:08: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:08: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:57:08: #2 alternative fragment length(s) may be 2,50,547 bps INFO @ Tue, 16 Jun 2020 09:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.05_model.r WARNING @ Tue, 16 Jun 2020 09:57:08: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:08: #2 You may need to consider one of the other alternative d(s): 2,50,547 WARNING @ Tue, 16 Jun 2020 09:57:08: #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 09:57:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:12: 4000000 INFO @ Tue, 16 Jun 2020 09:57:13: 9000000 INFO @ Tue, 16 Jun 2020 09:57:18: 5000000 INFO @ Tue, 16 Jun 2020 09:57:19: 10000000 INFO @ Tue, 16 Jun 2020 09:57:24: 6000000 INFO @ Tue, 16 Jun 2020 09:57:24: 11000000 INFO @ Tue, 16 Jun 2020 09:57:30: 7000000 INFO @ Tue, 16 Jun 2020 09:57:30: 12000000 INFO @ Tue, 16 Jun 2020 09:57:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:57:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:57:32: #1 total tags in treatment: 12335715 INFO @ Tue, 16 Jun 2020 09:57:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:32: #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 09:57:33: #1 tags after filtering in treatment: 12335715 INFO @ Tue, 16 Jun 2020 09:57:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:33: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 09:57:33: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:33: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:57:33: #2 alternative fragment length(s) may be 2,50,547 bps INFO @ Tue, 16 Jun 2020 09:57:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.10_model.r WARNING @ Tue, 16 Jun 2020 09:57:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:33: #2 You may need to consider one of the other alternative d(s): 2,50,547 WARNING @ Tue, 16 Jun 2020 09:57:33: #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 09:57:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:35: 8000000 INFO @ Tue, 16 Jun 2020 09:57:41: 9000000 INFO @ Tue, 16 Jun 2020 09:57:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.05_summits.bed INFO @ Tue, 16 Jun 2020 09:57:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:46: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:57:51: 11000000 INFO @ Tue, 16 Jun 2020 09:57:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:56: 12000000 INFO @ Tue, 16 Jun 2020 09:57:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:57:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:57:58: #1 total tags in treatment: 12335715 INFO @ Tue, 16 Jun 2020 09:57:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:58: #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 09:57:58: #1 tags after filtering in treatment: 12335715 INFO @ Tue, 16 Jun 2020 09:57:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:59: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 09:57:59: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:59: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:57:59: #2 alternative fragment length(s) may be 2,50,547 bps INFO @ Tue, 16 Jun 2020 09:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:59: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:59: #2 You may need to consider one of the other alternative d(s): 2,50,547 WARNING @ Tue, 16 Jun 2020 09:57:59: #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 09:57:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.10_summits.bed INFO @ Tue, 16 Jun 2020 09:58:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:58:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982087/SRX982087.20_summits.bed INFO @ Tue, 16 Jun 2020 09:58:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 1 millis CompletedMACS2peakCalling