Job ID = 6627438 SRX = SRX8521303 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:06:28 40475735 reads; of these: 40475735 (100.00%) were unpaired; of these: 33519463 (82.81%) aligned 0 times 5085118 (12.56%) aligned exactly 1 time 1871154 (4.62%) aligned >1 times 17.19% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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] 1097882 / 6956272 = 0.1578 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, 14 Jul 2020 11:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.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 @ Tue, 14 Jul 2020 11:42:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:42:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:42:36: 1000000 INFO @ Tue, 14 Jul 2020 11:42:44: 2000000 INFO @ Tue, 14 Jul 2020 11:42:52: 3000000 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, 14 Jul 2020 11:43:00: 4000000 INFO @ Tue, 14 Jul 2020 11:43:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.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 @ Tue, 14 Jul 2020 11:43:01: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:43:01: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:43:09: 1000000 INFO @ Tue, 14 Jul 2020 11:43:10: 5000000 INFO @ Tue, 14 Jul 2020 11:43:18: #1 tag size is determined as 69 bps INFO @ Tue, 14 Jul 2020 11:43:18: #1 tag size = 69 INFO @ Tue, 14 Jul 2020 11:43:18: #1 total tags in treatment: 5858390 INFO @ Tue, 14 Jul 2020 11:43:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:43:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:43:18: 2000000 INFO @ Tue, 14 Jul 2020 11:43:18: #1 tags after filtering in treatment: 5858195 INFO @ Tue, 14 Jul 2020 11:43:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:43:18: #1 finished! INFO @ Tue, 14 Jul 2020 11:43:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:43:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:43:19: #2 number of paired peaks: 662 WARNING @ Tue, 14 Jul 2020 11:43:19: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Tue, 14 Jul 2020 11:43:19: start model_add_line... INFO @ Tue, 14 Jul 2020 11:43:19: start X-correlation... INFO @ Tue, 14 Jul 2020 11:43:19: end of X-cor INFO @ Tue, 14 Jul 2020 11:43:19: #2 finished! INFO @ Tue, 14 Jul 2020 11:43:19: #2 predicted fragment length is 65 bps INFO @ Tue, 14 Jul 2020 11:43:19: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 14 Jul 2020 11:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.05_model.r WARNING @ Tue, 14 Jul 2020 11:43:19: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:43:19: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 14 Jul 2020 11:43:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:43:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:43:19: #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, 14 Jul 2020 11:43:25: 3000000 INFO @ Tue, 14 Jul 2020 11:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.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 @ Tue, 14 Jul 2020 11:43:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:43:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:43:33: 4000000 INFO @ Tue, 14 Jul 2020 11:43:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:43:36: 1000000 INFO @ Tue, 14 Jul 2020 11:43:42: 5000000 INFO @ Tue, 14 Jul 2020 11:43:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:43:44: 2000000 INFO @ Tue, 14 Jul 2020 11:43:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:43:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.05_summits.bed INFO @ Tue, 14 Jul 2020 11:43:44: Done! pass1 - making usageList (287 chroms): 33 millis pass2 - checking and writing primary data (1231 records, 4 fields): 72 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:43:49: #1 tag size is determined as 69 bps INFO @ Tue, 14 Jul 2020 11:43:49: #1 tag size = 69 INFO @ Tue, 14 Jul 2020 11:43:49: #1 total tags in treatment: 5858390 INFO @ Tue, 14 Jul 2020 11:43:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:43:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:43:49: #1 tags after filtering in treatment: 5858195 INFO @ Tue, 14 Jul 2020 11:43:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:43:49: #1 finished! INFO @ Tue, 14 Jul 2020 11:43:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:43:50: #2 number of paired peaks: 662 WARNING @ Tue, 14 Jul 2020 11:43:50: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Tue, 14 Jul 2020 11:43:50: start model_add_line... INFO @ Tue, 14 Jul 2020 11:43:50: start X-correlation... INFO @ Tue, 14 Jul 2020 11:43:50: end of X-cor INFO @ Tue, 14 Jul 2020 11:43:50: #2 finished! INFO @ Tue, 14 Jul 2020 11:43:50: #2 predicted fragment length is 65 bps INFO @ Tue, 14 Jul 2020 11:43:50: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 14 Jul 2020 11:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.10_model.r WARNING @ Tue, 14 Jul 2020 11:43:50: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:43:50: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 14 Jul 2020 11:43:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:43:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:43:51: 3000000 INFO @ Tue, 14 Jul 2020 11:43:58: 4000000 INFO @ Tue, 14 Jul 2020 11:44:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:44:05: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:44:11: #1 tag size is determined as 69 bps INFO @ Tue, 14 Jul 2020 11:44:11: #1 tag size = 69 INFO @ Tue, 14 Jul 2020 11:44:11: #1 total tags in treatment: 5858390 INFO @ Tue, 14 Jul 2020 11:44:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:44:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:44:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:44:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:44:12: #1 tags after filtering in treatment: 5858195 INFO @ Tue, 14 Jul 2020 11:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:44:12: #1 finished! INFO @ Tue, 14 Jul 2020 11:44:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:44:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.10_summits.bed INFO @ Tue, 14 Jul 2020 11:44:12: Done! INFO @ Tue, 14 Jul 2020 11:44:13: #2 number of paired peaks: 662 WARNING @ Tue, 14 Jul 2020 11:44:13: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Tue, 14 Jul 2020 11:44:13: start model_add_line... INFO @ Tue, 14 Jul 2020 11:44:13: start X-correlation... INFO @ Tue, 14 Jul 2020 11:44:13: end of X-cor INFO @ Tue, 14 Jul 2020 11:44:13: #2 finished! INFO @ Tue, 14 Jul 2020 11:44:13: #2 predicted fragment length is 65 bps INFO @ Tue, 14 Jul 2020 11:44:13: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 14 Jul 2020 11:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.20_model.r WARNING @ Tue, 14 Jul 2020 11:44:13: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:44:13: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 14 Jul 2020 11:44:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:44:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:44:13: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (155 chroms): 33 millis pass2 - checking and writing primary data (464 records, 4 fields): 73 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:44:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:44:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:44:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:44:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521303/SRX8521303.20_summits.bed INFO @ Tue, 14 Jul 2020 11:44:36: Done! pass1 - making usageList (91 chroms): 33 millis pass2 - checking and writing primary data (179 records, 4 fields): 38 millis CompletedMACS2peakCalling