Job ID = 6455033 SRX = SRX2642384 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:36:44 prefetch.2.10.7: 1) Downloading 'SRR5345724'... 2020-06-21T09:36:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:37:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:37:51 prefetch.2.10.7: 'SRR5345724' is valid 2020-06-21T09:37:51 prefetch.2.10.7: 1) 'SRR5345724' was downloaded successfully 2020-06-21T09:37:51 prefetch.2.10.7: 'SRR5345724' has 0 unresolved dependencies Read 2937296 spots for SRR5345724/SRR5345724.sra Written 2937296 spots for SRR5345724/SRR5345724.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: 00:01:26 2937296 reads; of these: 2937296 (100.00%) were unpaired; of these: 400630 (13.64%) aligned 0 times 1852581 (63.07%) aligned exactly 1 time 684085 (23.29%) aligned >1 times 86.36% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 142778 / 2536666 = 0.0563 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 18:41:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.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 18:41:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:10: 1000000 INFO @ Sun, 21 Jun 2020 18:41:19: 2000000 INFO @ Sun, 21 Jun 2020 18:41:23: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:41:23: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:41:23: #1 total tags in treatment: 2393888 INFO @ Sun, 21 Jun 2020 18:41:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:23: #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 18:41:24: #1 tags after filtering in treatment: 2393836 INFO @ Sun, 21 Jun 2020 18:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:24: #2 number of paired peaks: 648 WARNING @ Sun, 21 Jun 2020 18:41:24: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 21 Jun 2020 18:41:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:24: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:41:24: #2 alternative fragment length(s) may be 106,525 bps INFO @ Sun, 21 Jun 2020 18:41:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.05_model.r WARNING @ Sun, 21 Jun 2020 18:41:24: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:41:24: #2 You may need to consider one of the other alternative d(s): 106,525 WARNING @ Sun, 21 Jun 2020 18:41:24: #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 18:41:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:24: #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 @ Sun, 21 Jun 2020 18:41:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.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 18:41:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:41:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:41:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.05_summits.bed INFO @ Sun, 21 Jun 2020 18:41:33: Done! pass1 - making usageList (314 chroms): 1 millis pass2 - checking and writing primary data (561 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:41:39: 1000000 INFO @ Sun, 21 Jun 2020 18:41:49: 2000000 INFO @ Sun, 21 Jun 2020 18:41:53: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:41:53: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:41:53: #1 total tags in treatment: 2393888 INFO @ Sun, 21 Jun 2020 18:41:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:53: #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 18:41:53: #1 tags after filtering in treatment: 2393836 INFO @ Sun, 21 Jun 2020 18:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:53: #2 number of paired peaks: 648 WARNING @ Sun, 21 Jun 2020 18:41:53: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 21 Jun 2020 18:41:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:53: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:41:53: #2 alternative fragment length(s) may be 106,525 bps INFO @ Sun, 21 Jun 2020 18:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.10_model.r WARNING @ Sun, 21 Jun 2020 18:41:53: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:41:53: #2 You may need to consider one of the other alternative d(s): 106,525 WARNING @ Sun, 21 Jun 2020 18:41:53: #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 18:41:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:53: #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 @ Sun, 21 Jun 2020 18:41:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.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 18:42:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.10_summits.bed INFO @ Sun, 21 Jun 2020 18:42:02: Done! pass1 - making usageList (169 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:42:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:42:18: 2000000 INFO @ Sun, 21 Jun 2020 18:42:22: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:42:22: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:42:22: #1 total tags in treatment: 2393888 INFO @ Sun, 21 Jun 2020 18:42:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:42:22: #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 18:42:22: #1 tags after filtering in treatment: 2393836 INFO @ Sun, 21 Jun 2020 18:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:42:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:42:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:42:22: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:42:22: #2 number of paired peaks: 648 WARNING @ Sun, 21 Jun 2020 18:42:22: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 21 Jun 2020 18:42:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:42:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:42:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:42:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:42:22: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:42:22: #2 alternative fragment length(s) may be 106,525 bps INFO @ Sun, 21 Jun 2020 18:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.20_model.r WARNING @ Sun, 21 Jun 2020 18:42:22: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:42:22: #2 You may need to consider one of the other alternative d(s): 106,525 WARNING @ Sun, 21 Jun 2020 18:42:22: #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 18:42:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:42:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:42:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642384/SRX2642384.20_summits.bed INFO @ Sun, 21 Jun 2020 18:42:31: Done! pass1 - making usageList (105 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 5 millis CompletedMACS2peakCalling