Job ID = 6627444 SRX = SRX8521306 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: 00:09:23 56468412 reads; of these: 56468412 (100.00%) were unpaired; of these: 46648495 (82.61%) aligned 0 times 6662700 (11.80%) aligned exactly 1 time 3157217 (5.59%) aligned >1 times 17.39% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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] 2111256 / 9819917 = 0.2150 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 11:41:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.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 11:41:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:41:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:41:49: 1000000 INFO @ Tue, 14 Jul 2020 11:41:55: 2000000 INFO @ Tue, 14 Jul 2020 11:42:01: 3000000 INFO @ Tue, 14 Jul 2020 11:42:06: 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 @ Tue, 14 Jul 2020 11:42:12: 5000000 INFO @ Tue, 14 Jul 2020 11:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.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 11:42:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:42:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:42:18: 6000000 INFO @ Tue, 14 Jul 2020 11:42:20: 1000000 INFO @ Tue, 14 Jul 2020 11:42:25: 7000000 INFO @ Tue, 14 Jul 2020 11:42:27: 2000000 INFO @ Tue, 14 Jul 2020 11:42:30: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:42:30: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:42:30: #1 total tags in treatment: 7708661 INFO @ Tue, 14 Jul 2020 11:42:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:42:30: #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 11:42:31: #1 tags after filtering in treatment: 7708522 INFO @ Tue, 14 Jul 2020 11:42:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:42:31: #1 finished! INFO @ Tue, 14 Jul 2020 11:42:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:42:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:42:31: #2 number of paired peaks: 412 WARNING @ Tue, 14 Jul 2020 11:42:31: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 14 Jul 2020 11:42:31: start model_add_line... INFO @ Tue, 14 Jul 2020 11:42:31: start X-correlation... INFO @ Tue, 14 Jul 2020 11:42:31: end of X-cor INFO @ Tue, 14 Jul 2020 11:42:31: #2 finished! INFO @ Tue, 14 Jul 2020 11:42:31: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 11:42:31: #2 alternative fragment length(s) may be 4,13,64,518,551 bps INFO @ Tue, 14 Jul 2020 11:42:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.05_model.r WARNING @ Tue, 14 Jul 2020 11:42:31: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:42:31: #2 You may need to consider one of the other alternative d(s): 4,13,64,518,551 WARNING @ Tue, 14 Jul 2020 11:42:31: #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 11:42:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:42:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:42:33: 3000000 INFO @ Tue, 14 Jul 2020 11:42:40: 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 @ Tue, 14 Jul 2020 11:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.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 11:42:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:42:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:42:46: 5000000 INFO @ Tue, 14 Jul 2020 11:42:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:42:50: 1000000 INFO @ Tue, 14 Jul 2020 11:42:53: 6000000 INFO @ Tue, 14 Jul 2020 11:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.05_summits.bed INFO @ Tue, 14 Jul 2020 11:42:55: Done! pass1 - making usageList (290 chroms): 0 millis pass2 - checking and writing primary data (764 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:42:57: 2000000 INFO @ Tue, 14 Jul 2020 11:43:00: 7000000 INFO @ Tue, 14 Jul 2020 11:43:03: 3000000 INFO @ Tue, 14 Jul 2020 11:43:04: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:43:04: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:43:04: #1 total tags in treatment: 7708661 INFO @ Tue, 14 Jul 2020 11:43:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:43:04: #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 11:43:05: #1 tags after filtering in treatment: 7708522 INFO @ Tue, 14 Jul 2020 11:43:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:43:05: #1 finished! INFO @ Tue, 14 Jul 2020 11:43:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:43:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:43:05: #2 number of paired peaks: 412 WARNING @ Tue, 14 Jul 2020 11:43:05: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 14 Jul 2020 11:43:05: start model_add_line... INFO @ Tue, 14 Jul 2020 11:43:05: start X-correlation... INFO @ Tue, 14 Jul 2020 11:43:05: end of X-cor INFO @ Tue, 14 Jul 2020 11:43:05: #2 finished! INFO @ Tue, 14 Jul 2020 11:43:05: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 11:43:05: #2 alternative fragment length(s) may be 4,13,64,518,551 bps INFO @ Tue, 14 Jul 2020 11:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.10_model.r WARNING @ Tue, 14 Jul 2020 11:43:05: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:43:05: #2 You may need to consider one of the other alternative d(s): 4,13,64,518,551 WARNING @ Tue, 14 Jul 2020 11:43:05: #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 11:43:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:43:09: 4000000 INFO @ Tue, 14 Jul 2020 11:43:15: 5000000 INFO @ Tue, 14 Jul 2020 11:43:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:43:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:43:28: 7000000 INFO @ Tue, 14 Jul 2020 11:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:43:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.10_summits.bed INFO @ Tue, 14 Jul 2020 11:43:29: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:43:32: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:43:32: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:43:32: #1 total tags in treatment: 7708661 INFO @ Tue, 14 Jul 2020 11:43:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:43:32: #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 11:43:32: #1 tags after filtering in treatment: 7708522 INFO @ Tue, 14 Jul 2020 11:43:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:43:32: #1 finished! INFO @ Tue, 14 Jul 2020 11:43:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:43:33: #2 number of paired peaks: 412 WARNING @ Tue, 14 Jul 2020 11:43:33: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 14 Jul 2020 11:43:33: start model_add_line... INFO @ Tue, 14 Jul 2020 11:43:33: start X-correlation... INFO @ Tue, 14 Jul 2020 11:43:33: end of X-cor INFO @ Tue, 14 Jul 2020 11:43:33: #2 finished! INFO @ Tue, 14 Jul 2020 11:43:33: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 11:43:33: #2 alternative fragment length(s) may be 4,13,64,518,551 bps INFO @ Tue, 14 Jul 2020 11:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.20_model.r WARNING @ Tue, 14 Jul 2020 11:43:33: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:43:33: #2 You may need to consider one of the other alternative d(s): 4,13,64,518,551 WARNING @ Tue, 14 Jul 2020 11:43:33: #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 11:43:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:43:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:43:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:43:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:43:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:43:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521306/SRX8521306.20_summits.bed INFO @ Tue, 14 Jul 2020 11:43:57: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 4 millis CompletedMACS2peakCalling