Job ID = 6366118 SRX = SRX065634 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:52 prefetch.2.10.7: 1) Downloading 'SRR217340'... 2020-06-15T22:48:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:26 prefetch.2.10.7: 'SRR217340' is valid 2020-06-15T22:49:26 prefetch.2.10.7: 1) 'SRR217340' was downloaded successfully Read 6386561 spots for SRR217340/SRR217340.sra Written 6386561 spots for SRR217340/SRR217340.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: 00:01:01 6386561 reads; of these: 6386561 (100.00%) were unpaired; of these: 88529 (1.39%) aligned 0 times 5335992 (83.55%) aligned exactly 1 time 962040 (15.06%) aligned >1 times 98.61% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 585872 / 6298032 = 0.0930 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 07:52:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.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 07:52:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:34: 1000000 INFO @ Tue, 16 Jun 2020 07:52:40: 2000000 INFO @ Tue, 16 Jun 2020 07:52:47: 3000000 INFO @ Tue, 16 Jun 2020 07:52:54: 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 07:52:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.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 07:52:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:01: 5000000 INFO @ Tue, 16 Jun 2020 07:53:04: 1000000 INFO @ Tue, 16 Jun 2020 07:53:06: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:53:06: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:53:06: #1 total tags in treatment: 5712160 INFO @ Tue, 16 Jun 2020 07:53:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:06: #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 07:53:06: #1 tags after filtering in treatment: 5712160 INFO @ Tue, 16 Jun 2020 07:53:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:06: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 07:53:06: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:06: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:53:06: #2 alternative fragment length(s) may be 3,33,524,550,574 bps INFO @ Tue, 16 Jun 2020 07:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.05_model.r WARNING @ Tue, 16 Jun 2020 07:53:06: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:06: #2 You may need to consider one of the other alternative d(s): 3,33,524,550,574 WARNING @ Tue, 16 Jun 2020 07:53:06: #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 07:53:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:11: 2000000 INFO @ Tue, 16 Jun 2020 07:53:17: 3000000 INFO @ Tue, 16 Jun 2020 07:53:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:24: 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 07:53:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (302 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.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 07:53:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:31: 5000000 INFO @ Tue, 16 Jun 2020 07:53:34: 1000000 INFO @ Tue, 16 Jun 2020 07:53:36: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:53:36: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:53:36: #1 total tags in treatment: 5712160 INFO @ Tue, 16 Jun 2020 07:53:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:36: #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 07:53:36: #1 tags after filtering in treatment: 5712160 INFO @ Tue, 16 Jun 2020 07:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:36: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 07:53:36: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:37: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:53:37: #2 alternative fragment length(s) may be 3,33,524,550,574 bps INFO @ Tue, 16 Jun 2020 07:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.10_model.r WARNING @ Tue, 16 Jun 2020 07:53:37: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:37: #2 You may need to consider one of the other alternative d(s): 3,33,524,550,574 WARNING @ Tue, 16 Jun 2020 07:53:37: #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 07:53:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:41: 2000000 INFO @ Tue, 16 Jun 2020 07:53:47: 3000000 INFO @ Tue, 16 Jun 2020 07:53:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:53:54: 4000000 INFO @ Tue, 16 Jun 2020 07:53:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (129 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:00: 5000000 INFO @ Tue, 16 Jun 2020 07:54:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:54:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:54:04: #1 total tags in treatment: 5712160 INFO @ Tue, 16 Jun 2020 07:54:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:04: #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 07:54:04: #1 tags after filtering in treatment: 5712160 INFO @ Tue, 16 Jun 2020 07:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:05: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 07:54:05: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:05: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:54:05: #2 alternative fragment length(s) may be 3,33,524,550,574 bps INFO @ Tue, 16 Jun 2020 07:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.20_model.r WARNING @ Tue, 16 Jun 2020 07:54:05: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:05: #2 You may need to consider one of the other alternative d(s): 3,33,524,550,574 WARNING @ Tue, 16 Jun 2020 07:54:05: #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 07:54:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065634/SRX065634.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling