Job ID = 6367062 SRX = SRX276920 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:11:46 prefetch.2.10.7: 1) Downloading 'SRR849526'... 2020-06-15T23:11:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:22 prefetch.2.10.7: 'SRR849526' is valid 2020-06-15T23:12:22 prefetch.2.10.7: 1) 'SRR849526' was downloaded successfully Read 5840666 spots for SRR849526/SRR849526.sra Written 5840666 spots for SRR849526/SRR849526.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: 00:00:45 5840666 reads; of these: 5840666 (100.00%) were unpaired; of these: 2263581 (38.76%) aligned 0 times 3009732 (51.53%) aligned exactly 1 time 567353 (9.71%) aligned >1 times 61.24% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 344337 / 3577085 = 0.0963 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 08:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.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 08:14:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:43: 1000000 INFO @ Tue, 16 Jun 2020 08:14:49: 2000000 INFO @ Tue, 16 Jun 2020 08:14:54: 3000000 INFO @ Tue, 16 Jun 2020 08:14:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:14:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:14:55: #1 total tags in treatment: 3232748 INFO @ Tue, 16 Jun 2020 08:14:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:55: #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 08:14:55: #1 tags after filtering in treatment: 3232748 INFO @ Tue, 16 Jun 2020 08:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:56: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:14:56: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:56: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:14:56: #2 alternative fragment length(s) may be 31,144,519 bps INFO @ Tue, 16 Jun 2020 08:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.05_model.r WARNING @ Tue, 16 Jun 2020 08:14:56: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:56: #2 You may need to consider one of the other alternative d(s): 31,144,519 WARNING @ Tue, 16 Jun 2020 08:14:56: #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 08:14:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:03: #3 Call peaks for each chromosome... 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 08:15:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.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 08:15:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:14: 1000000 INFO @ Tue, 16 Jun 2020 08:15:21: 2000000 INFO @ Tue, 16 Jun 2020 08:15:27: 3000000 INFO @ Tue, 16 Jun 2020 08:15:29: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:29: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:29: #1 total tags in treatment: 3232748 INFO @ Tue, 16 Jun 2020 08:15:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:29: #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 08:15:29: #1 tags after filtering in treatment: 3232748 INFO @ Tue, 16 Jun 2020 08:15:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:29: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:15:29: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:29: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:15:29: #2 alternative fragment length(s) may be 31,144,519 bps INFO @ Tue, 16 Jun 2020 08:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:29: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:29: #2 You may need to consider one of the other alternative d(s): 31,144,519 WARNING @ Tue, 16 Jun 2020 08:15:29: #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 08:15:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:29: #3 Pre-compute pvalue-qvalue table... 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 08:15:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.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 08:15:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (148 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:45: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:51: 2000000 INFO @ Tue, 16 Jun 2020 08:15:58: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:59: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:59: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:59: #1 total tags in treatment: 3232748 INFO @ Tue, 16 Jun 2020 08:15:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:59: #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 08:15:59: #1 tags after filtering in treatment: 3232748 INFO @ Tue, 16 Jun 2020 08:15:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:00: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:16:00: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:00: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:16:00: #2 alternative fragment length(s) may be 31,144,519 bps INFO @ Tue, 16 Jun 2020 08:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.20_model.r WARNING @ Tue, 16 Jun 2020 08:16:00: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:00: #2 You may need to consider one of the other alternative d(s): 31,144,519 WARNING @ Tue, 16 Jun 2020 08:16:00: #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 08:16:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX276920/SRX276920.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 millis CompletedMACS2peakCalling