Job ID = 6365974 SRX = SRX043985 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:25:29 prefetch.2.10.7: 1) Downloading 'SRR107560'... 2020-06-15T22:25:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:26:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:26:09 prefetch.2.10.7: 'SRR107560' is valid 2020-06-15T22:26:09 prefetch.2.10.7: 1) 'SRR107560' was downloaded successfully Read 6024710 spots for SRR107560/SRR107560.sra Written 6024710 spots for SRR107560/SRR107560.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: 00:00:47 6024710 reads; of these: 6024710 (100.00%) were unpaired; of these: 2524123 (41.90%) aligned 0 times 3060215 (50.79%) aligned exactly 1 time 440372 (7.31%) aligned >1 times 58.10% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 207957 / 3500587 = 0.0594 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 07:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.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 07:28:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:28:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:28:45: 1000000 INFO @ Tue, 16 Jun 2020 07:28:51: 2000000 INFO @ Tue, 16 Jun 2020 07:28:58: 3000000 INFO @ Tue, 16 Jun 2020 07:29:00: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:29:00: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:29:00: #1 total tags in treatment: 3292630 INFO @ Tue, 16 Jun 2020 07:29:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:29:00: #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 07:29:00: #1 tags after filtering in treatment: 3292630 INFO @ Tue, 16 Jun 2020 07:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:29:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:29:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:29:00: #2 number of paired peaks: 215 WARNING @ Tue, 16 Jun 2020 07:29:00: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 16 Jun 2020 07:29:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:29:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:29:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:29:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:29:00: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:29:00: #2 alternative fragment length(s) may be 4,39,99,106,116,376,492 bps INFO @ Tue, 16 Jun 2020 07:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.05_model.r WARNING @ Tue, 16 Jun 2020 07:29:00: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:29:00: #2 You may need to consider one of the other alternative d(s): 4,39,99,106,116,376,492 WARNING @ Tue, 16 Jun 2020 07:29:00: #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 07:29:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:29:00: #3 Pre-compute pvalue-qvalue table... 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 07:29:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.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 07:29:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:29:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:29:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:29:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:29:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.05_summits.bed INFO @ Tue, 16 Jun 2020 07:29:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:29:15: 1000000 INFO @ Tue, 16 Jun 2020 07:29:21: 2000000 INFO @ Tue, 16 Jun 2020 07:29:28: 3000000 INFO @ Tue, 16 Jun 2020 07:29:29: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:29:29: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:29:29: #1 total tags in treatment: 3292630 INFO @ Tue, 16 Jun 2020 07:29:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:29:29: #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 07:29:30: #1 tags after filtering in treatment: 3292630 INFO @ Tue, 16 Jun 2020 07:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:29:30: #1 finished! INFO @ Tue, 16 Jun 2020 07:29:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:29:30: #2 number of paired peaks: 215 WARNING @ Tue, 16 Jun 2020 07:29:30: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 16 Jun 2020 07:29:30: start model_add_line... INFO @ Tue, 16 Jun 2020 07:29:30: start X-correlation... INFO @ Tue, 16 Jun 2020 07:29:30: end of X-cor INFO @ Tue, 16 Jun 2020 07:29:30: #2 finished! INFO @ Tue, 16 Jun 2020 07:29:30: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:29:30: #2 alternative fragment length(s) may be 4,39,99,106,116,376,492 bps INFO @ Tue, 16 Jun 2020 07:29:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.10_model.r WARNING @ Tue, 16 Jun 2020 07:29:30: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:29:30: #2 You may need to consider one of the other alternative d(s): 4,39,99,106,116,376,492 WARNING @ Tue, 16 Jun 2020 07:29:30: #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 07:29:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:29:30: #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 07:29:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.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 07:29:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:29:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:29:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:29:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:29:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.10_summits.bed INFO @ Tue, 16 Jun 2020 07:29:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 0 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:29:45: 1000000 INFO @ Tue, 16 Jun 2020 07:29:52: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:29:58: 3000000 INFO @ Tue, 16 Jun 2020 07:30:00: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:30:00: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:30:00: #1 total tags in treatment: 3292630 INFO @ Tue, 16 Jun 2020 07:30:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:30:00: #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 07:30:00: #1 tags after filtering in treatment: 3292630 INFO @ Tue, 16 Jun 2020 07:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:30:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:30:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:30:01: #2 number of paired peaks: 215 WARNING @ Tue, 16 Jun 2020 07:30:01: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 16 Jun 2020 07:30:01: start model_add_line... INFO @ Tue, 16 Jun 2020 07:30:01: start X-correlation... INFO @ Tue, 16 Jun 2020 07:30:01: end of X-cor INFO @ Tue, 16 Jun 2020 07:30:01: #2 finished! INFO @ Tue, 16 Jun 2020 07:30:01: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:30:01: #2 alternative fragment length(s) may be 4,39,99,106,116,376,492 bps INFO @ Tue, 16 Jun 2020 07:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.20_model.r WARNING @ Tue, 16 Jun 2020 07:30:01: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:30:01: #2 You may need to consider one of the other alternative d(s): 4,39,99,106,116,376,492 WARNING @ Tue, 16 Jun 2020 07:30:01: #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 07:30:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:30:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:30:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:30:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:30:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:30:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043985/SRX043985.20_summits.bed INFO @ Tue, 16 Jun 2020 07:30:12: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling