Job ID = 6455027 SRX = SRX2642378 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:41:10 prefetch.2.10.7: 1) Downloading 'SRR5345718'... 2020-06-21T09:41:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:42:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:42:10 prefetch.2.10.7: 'SRR5345718' is valid 2020-06-21T09:42:10 prefetch.2.10.7: 1) 'SRR5345718' was downloaded successfully 2020-06-21T09:42:10 prefetch.2.10.7: 'SRR5345718' has 0 unresolved dependencies Read 2905050 spots for SRR5345718/SRR5345718.sra Written 2905050 spots for SRR5345718/SRR5345718.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: 00:01:28 2905050 reads; of these: 2905050 (100.00%) were unpaired; of these: 306143 (10.54%) aligned 0 times 1881002 (64.75%) aligned exactly 1 time 717905 (24.71%) aligned >1 times 89.46% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 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] 130681 / 2598907 = 0.0503 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 18:45:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.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 18:45:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:34: 1000000 INFO @ Sun, 21 Jun 2020 18:45:40: 2000000 INFO @ Sun, 21 Jun 2020 18:45:44: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 18:45:44: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 18:45:44: #1 total tags in treatment: 2468226 INFO @ Sun, 21 Jun 2020 18:45:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:44: #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 18:45:44: #1 tags after filtering in treatment: 2468186 INFO @ Sun, 21 Jun 2020 18:45:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:45: #2 number of paired peaks: 469 WARNING @ Sun, 21 Jun 2020 18:45:45: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:45: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 18:45:45: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 18:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.05_model.r WARNING @ Sun, 21 Jun 2020 18:45:45: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:45: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sun, 21 Jun 2020 18:45:45: #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 18:45:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:54: Done! pass1 - making usageList (369 chroms): 1 millis pass2 - checking and writing primary data (664 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 18:45:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.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 18:45:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:04: 1000000 INFO @ Sun, 21 Jun 2020 18:46:10: 2000000 INFO @ Sun, 21 Jun 2020 18:46:14: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 18:46:14: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 18:46:14: #1 total tags in treatment: 2468226 INFO @ Sun, 21 Jun 2020 18:46:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:14: #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 18:46:14: #1 tags after filtering in treatment: 2468186 INFO @ Sun, 21 Jun 2020 18:46:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:14: #2 number of paired peaks: 469 WARNING @ Sun, 21 Jun 2020 18:46:14: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:14: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 18:46:14: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 18:46:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.10_model.r WARNING @ Sun, 21 Jun 2020 18:46:14: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:14: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sun, 21 Jun 2020 18:46:14: #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 18:46:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:23: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (325 records, 4 fields): 8 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 18:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.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 18:46:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:33: 1000000 INFO @ Sun, 21 Jun 2020 18:46:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:46:44: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 18:46:44: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 18:46:44: #1 total tags in treatment: 2468226 INFO @ Sun, 21 Jun 2020 18:46:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:44: #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 18:46:44: #1 tags after filtering in treatment: 2468186 INFO @ Sun, 21 Jun 2020 18:46:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:44: #2 number of paired peaks: 469 WARNING @ Sun, 21 Jun 2020 18:46:44: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:44: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:44: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 18:46:44: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 18:46:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.20_model.r WARNING @ Sun, 21 Jun 2020 18:46:44: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:44: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sun, 21 Jun 2020 18:46:44: #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 18:46:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:46:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642378/SRX2642378.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:53: Done! pass1 - making usageList (107 chroms): 1 millis pass2 - checking and writing primary data (160 records, 4 fields): 5 millis CompletedMACS2peakCalling