Job ID = 6454234 SRX = SRX193313 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:01:50 prefetch.2.10.7: 1) Downloading 'SRR585046'... 2020-06-21T09:01:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:02:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:02:48 prefetch.2.10.7: 'SRR585046' is valid 2020-06-21T09:02:48 prefetch.2.10.7: 1) 'SRR585046' was downloaded successfully Read 7892809 spots for SRR585046/SRR585046.sra Written 7892809 spots for SRR585046/SRR585046.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: 00:02:38 7892809 reads; of these: 7892809 (100.00%) were unpaired; of these: 261610 (3.31%) aligned 0 times 5284691 (66.96%) aligned exactly 1 time 2346508 (29.73%) aligned >1 times 96.69% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 840157 / 7631199 = 0.1101 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 @ Sun, 21 Jun 2020 18:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:08:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:08:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:08:51: 1000000 INFO @ Sun, 21 Jun 2020 18:08:57: 2000000 INFO @ Sun, 21 Jun 2020 18:09:04: 3000000 INFO @ Sun, 21 Jun 2020 18:09:10: 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 @ Sun, 21 Jun 2020 18:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:09:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:16: 5000000 INFO @ Sun, 21 Jun 2020 18:09:21: 1000000 INFO @ Sun, 21 Jun 2020 18:09:24: 6000000 INFO @ Sun, 21 Jun 2020 18:09:28: 2000000 INFO @ Sun, 21 Jun 2020 18:09:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:09:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:09:30: #1 total tags in treatment: 6791042 INFO @ Sun, 21 Jun 2020 18:09:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:09:31: #1 tags after filtering in treatment: 6790900 INFO @ Sun, 21 Jun 2020 18:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:31: #2 number of paired peaks: 978 WARNING @ Sun, 21 Jun 2020 18:09:31: Fewer paired peaks (978) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 978 pairs to build model! INFO @ Sun, 21 Jun 2020 18:09:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:31: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 18:09:31: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 21 Jun 2020 18:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.05_model.r WARNING @ Sun, 21 Jun 2020 18:09:31: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:09:31: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 21 Jun 2020 18:09:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:09:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:09:35: 3000000 INFO @ Sun, 21 Jun 2020 18:09:41: 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 @ Sun, 21 Jun 2020 18:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:09:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:48: 5000000 INFO @ Sun, 21 Jun 2020 18:09:52: 1000000 INFO @ Sun, 21 Jun 2020 18:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.05_summits.bed INFO @ Sun, 21 Jun 2020 18:09:53: Done! pass1 - making usageList (548 chroms): 2 millis pass2 - checking and writing primary data (1876 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:09:55: 6000000 INFO @ Sun, 21 Jun 2020 18:09:58: 2000000 INFO @ Sun, 21 Jun 2020 18:10:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:10:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:10:01: #1 total tags in treatment: 6791042 INFO @ Sun, 21 Jun 2020 18:10:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:10:01: #1 tags after filtering in treatment: 6790900 INFO @ Sun, 21 Jun 2020 18:10:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:02: #2 number of paired peaks: 978 WARNING @ Sun, 21 Jun 2020 18:10:02: Fewer paired peaks (978) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 978 pairs to build model! INFO @ Sun, 21 Jun 2020 18:10:02: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:02: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:02: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 18:10:02: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 21 Jun 2020 18:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.10_model.r WARNING @ Sun, 21 Jun 2020 18:10:02: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:10:02: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 21 Jun 2020 18:10:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:10:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:05: 3000000 INFO @ Sun, 21 Jun 2020 18:10:12: 4000000 INFO @ Sun, 21 Jun 2020 18:10:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:19: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.10_summits.bed INFO @ Sun, 21 Jun 2020 18:10:24: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (772 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:10:27: 6000000 INFO @ Sun, 21 Jun 2020 18:10:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:10:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:10:33: #1 total tags in treatment: 6791042 INFO @ Sun, 21 Jun 2020 18:10:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:10:33: #1 tags after filtering in treatment: 6790900 INFO @ Sun, 21 Jun 2020 18:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:34: #2 number of paired peaks: 978 WARNING @ Sun, 21 Jun 2020 18:10:34: Fewer paired peaks (978) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 978 pairs to build model! INFO @ Sun, 21 Jun 2020 18:10:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:34: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 18:10:34: #2 alternative fragment length(s) may be 66 bps INFO @ Sun, 21 Jun 2020 18:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.20_model.r WARNING @ Sun, 21 Jun 2020 18:10:34: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:10:34: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sun, 21 Jun 2020 18:10:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:10:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:10:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193313/SRX193313.20_summits.bed INFO @ Sun, 21 Jun 2020 18:10:56: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (374 records, 4 fields): 10 millis CompletedMACS2peakCalling