Job ID = 6454611 SRX = SRX2399656 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:22:44 prefetch.2.10.7: 1) Downloading 'SRR5081490'... 2020-06-21T09:22:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:25:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:25:05 prefetch.2.10.7: 'SRR5081490' is valid 2020-06-21T09:25:05 prefetch.2.10.7: 1) 'SRR5081490' was downloaded successfully 2020-06-21T09:25:05 prefetch.2.10.7: 'SRR5081490' has 0 unresolved dependencies Read 17861866 spots for SRR5081490/SRR5081490.sra Written 17861866 spots for SRR5081490/SRR5081490.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: 00:03:43 17861866 reads; of these: 17861866 (100.00%) were unpaired; of these: 10452881 (58.52%) aligned 0 times 4862774 (27.22%) aligned exactly 1 time 2546211 (14.26%) aligned >1 times 41.48% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 1421556 / 7408985 = 0.1919 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 18:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.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 18:32:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:09: 1000000 INFO @ Sun, 21 Jun 2020 18:32:15: 2000000 INFO @ Sun, 21 Jun 2020 18:32:20: 3000000 INFO @ Sun, 21 Jun 2020 18:32:25: 4000000 INFO @ Sun, 21 Jun 2020 18:32:31: 5000000 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 18:32:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.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 18:32:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:32:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:32:37: #1 total tags in treatment: 5987429 INFO @ Sun, 21 Jun 2020 18:32:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:37: #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 18:32:37: #1 tags after filtering in treatment: 5987425 INFO @ Sun, 21 Jun 2020 18:32:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:38: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 18:32:38: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 18:32:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:38: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:32:38: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 18:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.05_model.r WARNING @ Sun, 21 Jun 2020 18:32:38: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:38: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 18:32:38: #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 18:32:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:39: 1000000 INFO @ Sun, 21 Jun 2020 18:32:45: 2000000 INFO @ Sun, 21 Jun 2020 18:32:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:51: 3000000 INFO @ Sun, 21 Jun 2020 18:32:57: 4000000 INFO @ Sun, 21 Jun 2020 18:32:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.05_summits.bed INFO @ Sun, 21 Jun 2020 18:32:57: Done! pass1 - making usageList (491 chroms): 2 millis pass2 - checking and writing primary data (2812 records, 4 fields): 14 millis CompletedMACS2peakCalling 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 18:33:03: 5000000 INFO @ Sun, 21 Jun 2020 18:33:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.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 18:33:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:33:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:33:09: #1 total tags in treatment: 5987429 INFO @ Sun, 21 Jun 2020 18:33:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:09: #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 18:33:10: 1000000 INFO @ Sun, 21 Jun 2020 18:33:10: #1 tags after filtering in treatment: 5987425 INFO @ Sun, 21 Jun 2020 18:33:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:10: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 18:33:10: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 18:33:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:10: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:33:10: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 18:33:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.10_model.r WARNING @ Sun, 21 Jun 2020 18:33:10: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:10: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 18:33:10: #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 18:33:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:16: 2000000 INFO @ Sun, 21 Jun 2020 18:33:22: 3000000 INFO @ Sun, 21 Jun 2020 18:33:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:28: 4000000 INFO @ Sun, 21 Jun 2020 18:33:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.10_summits.bed INFO @ Sun, 21 Jun 2020 18:33:29: Done! pass1 - making usageList (286 chroms): 0 millis pass2 - checking and writing primary data (971 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:33:34: 5000000 INFO @ Sun, 21 Jun 2020 18:33:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:33:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:33:40: #1 total tags in treatment: 5987429 INFO @ Sun, 21 Jun 2020 18:33:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:40: #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 18:33:41: #1 tags after filtering in treatment: 5987425 INFO @ Sun, 21 Jun 2020 18:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:41: #2 number of paired peaks: 625 WARNING @ Sun, 21 Jun 2020 18:33:41: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Sun, 21 Jun 2020 18:33:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:41: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:33:41: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 18:33:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.20_model.r WARNING @ Sun, 21 Jun 2020 18:33:41: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:41: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 18:33:41: #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 18:33:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:33:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399656/SRX2399656.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:01: Done! pass1 - making usageList (140 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 5 millis CompletedMACS2peakCalling