Job ID = 6529357 SRX = SRX202831 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: 00:03:13 8953061 reads; of these: 8953061 (100.00%) were unpaired; of these: 376561 (4.21%) aligned 0 times 7191365 (80.32%) aligned exactly 1 time 1385135 (15.47%) aligned >1 times 95.79% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 669267 / 8576500 = 0.0780 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, 30 Jun 2020 02:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.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, 30 Jun 2020 02:01:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:33: 1000000 INFO @ Tue, 30 Jun 2020 02:01:40: 2000000 INFO @ Tue, 30 Jun 2020 02:01:47: 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, 30 Jun 2020 02:01:55: 4000000 INFO @ Tue, 30 Jun 2020 02:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.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, 30 Jun 2020 02:01:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:02: 5000000 INFO @ Tue, 30 Jun 2020 02:02:03: 1000000 INFO @ Tue, 30 Jun 2020 02:02:09: 6000000 INFO @ Tue, 30 Jun 2020 02:02:11: 2000000 INFO @ Tue, 30 Jun 2020 02:02:17: 7000000 INFO @ Tue, 30 Jun 2020 02:02:18: 3000000 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, 30 Jun 2020 02:02:24: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 02:02:24: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 02:02:24: #1 total tags in treatment: 7907233 INFO @ Tue, 30 Jun 2020 02:02:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:02:25: #1 tags after filtering in treatment: 7907218 INFO @ Tue, 30 Jun 2020 02:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:25: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 02:02:25: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:25: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 02:02:25: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 30 Jun 2020 02:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.05_model.r WARNING @ Tue, 30 Jun 2020 02:02:25: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:02:25: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 30 Jun 2020 02:02:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:02:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.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, 30 Jun 2020 02:02:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:26: 4000000 INFO @ Tue, 30 Jun 2020 02:02:33: 1000000 INFO @ Tue, 30 Jun 2020 02:02:33: 5000000 INFO @ Tue, 30 Jun 2020 02:02:40: 2000000 INFO @ Tue, 30 Jun 2020 02:02:41: 6000000 INFO @ Tue, 30 Jun 2020 02:02:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:02:48: 3000000 INFO @ Tue, 30 Jun 2020 02:02:49: 7000000 INFO @ Tue, 30 Jun 2020 02:02:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:02:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:02:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.05_summits.bed INFO @ Tue, 30 Jun 2020 02:02:55: Done! pass1 - making usageList (165 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:02:55: 4000000 INFO @ Tue, 30 Jun 2020 02:02:56: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 02:02:56: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 02:02:56: #1 total tags in treatment: 7907233 INFO @ Tue, 30 Jun 2020 02:02:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:02:56: #1 tags after filtering in treatment: 7907218 INFO @ Tue, 30 Jun 2020 02:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:57: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 02:02:57: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:57: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 02:02:57: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 30 Jun 2020 02:02:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.10_model.r WARNING @ Tue, 30 Jun 2020 02:02:57: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:02:57: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 30 Jun 2020 02:02:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:02:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:02: 5000000 INFO @ Tue, 30 Jun 2020 02:03:09: 6000000 INFO @ Tue, 30 Jun 2020 02:03:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:03:17: 7000000 INFO @ Tue, 30 Jun 2020 02:03:24: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 02:03:24: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 02:03:24: #1 total tags in treatment: 7907233 INFO @ Tue, 30 Jun 2020 02:03:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:03:24: #1 tags after filtering in treatment: 7907218 INFO @ Tue, 30 Jun 2020 02:03:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:25: #2 number of paired peaks: 149 WARNING @ Tue, 30 Jun 2020 02:03:25: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:25: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 02:03:25: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 30 Jun 2020 02:03:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.20_model.r WARNING @ Tue, 30 Jun 2020 02:03:25: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:03:25: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 30 Jun 2020 02:03:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:03:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.10_summits.bed INFO @ Tue, 30 Jun 2020 02:03:26: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:03:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:03:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202831/SRX202831.20_summits.bed INFO @ Tue, 30 Jun 2020 02:03:55: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 5 millis CompletedMACS2peakCalling