Job ID = 14170969 SRX = SRX8689097 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: 00:01:32 6378269 reads; of these: 6378269 (100.00%) were unpaired; of these: 229339 (3.60%) aligned 0 times 5189729 (81.37%) aligned exactly 1 time 959201 (15.04%) aligned >1 times 96.40% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 271426 / 6148930 = 0.0441 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.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 @ Sat, 11 Dec 2021 09:09:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:09:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:02: 1000000 INFO @ Sat, 11 Dec 2021 09:10:09: 2000000 INFO @ Sat, 11 Dec 2021 09:10:16: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:10:23: 4000000 INFO @ Sat, 11 Dec 2021 09:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.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 @ Sat, 11 Dec 2021 09:10:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:10:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:31: 5000000 INFO @ Sat, 11 Dec 2021 09:10:32: 1000000 INFO @ Sat, 11 Dec 2021 09:10:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:38: #1 total tags in treatment: 5877504 INFO @ Sat, 11 Dec 2021 09:10:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:10:38: #1 tags after filtering in treatment: 5877282 INFO @ Sat, 11 Dec 2021 09:10:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:38: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:39: 2000000 INFO @ Sat, 11 Dec 2021 09:10:39: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 09:10:39: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 09:10:39: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:39: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:39: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:39: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:39: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 09:10:39: #2 alternative fragment length(s) may be 53,567 bps INFO @ Sat, 11 Dec 2021 09:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.05_model.r WARNING @ Sat, 11 Dec 2021 09:10:39: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:39: #2 You may need to consider one of the other alternative d(s): 53,567 WARNING @ Sat, 11 Dec 2021 09:10:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:10:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:10:45: 3000000 INFO @ Sat, 11 Dec 2021 09:10:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:51: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.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 @ Sat, 11 Dec 2021 09:10:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:10:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.05_summits.bed INFO @ Sat, 11 Dec 2021 09:10:57: Done! pass1 - making usageList (232 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:10:58: 5000000 INFO @ Sat, 11 Dec 2021 09:11:02: 1000000 INFO @ Sat, 11 Dec 2021 09:11:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:11:05: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:11:05: #1 total tags in treatment: 5877504 INFO @ Sat, 11 Dec 2021 09:11:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:11:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:11:05: #1 tags after filtering in treatment: 5877282 INFO @ Sat, 11 Dec 2021 09:11:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:11:05: #1 finished! INFO @ Sat, 11 Dec 2021 09:11:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:11:05: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 09:11:05: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 09:11:05: start model_add_line... INFO @ Sat, 11 Dec 2021 09:11:05: start X-correlation... INFO @ Sat, 11 Dec 2021 09:11:05: end of X-cor INFO @ Sat, 11 Dec 2021 09:11:05: #2 finished! INFO @ Sat, 11 Dec 2021 09:11:05: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 09:11:05: #2 alternative fragment length(s) may be 53,567 bps INFO @ Sat, 11 Dec 2021 09:11:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.10_model.r WARNING @ Sat, 11 Dec 2021 09:11:05: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:11:05: #2 You may need to consider one of the other alternative d(s): 53,567 WARNING @ Sat, 11 Dec 2021 09:11:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:11:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:11:08: 2000000 INFO @ Sat, 11 Dec 2021 09:11:15: 3000000 INFO @ Sat, 11 Dec 2021 09:11:17: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:11:21: 4000000 INFO @ Sat, 11 Dec 2021 09:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.10_summits.bed INFO @ Sat, 11 Dec 2021 09:11:23: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:11:28: 5000000 INFO @ Sat, 11 Dec 2021 09:11:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:11:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:11:34: #1 total tags in treatment: 5877504 INFO @ Sat, 11 Dec 2021 09:11:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:11:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:11:34: #1 tags after filtering in treatment: 5877282 INFO @ Sat, 11 Dec 2021 09:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:11:34: #1 finished! INFO @ Sat, 11 Dec 2021 09:11:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:11:34: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:11:34: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 09:11:34: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 09:11:34: start model_add_line... INFO @ Sat, 11 Dec 2021 09:11:34: start X-correlation... INFO @ Sat, 11 Dec 2021 09:11:34: end of X-cor INFO @ Sat, 11 Dec 2021 09:11:34: #2 finished! INFO @ Sat, 11 Dec 2021 09:11:34: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 09:11:34: #2 alternative fragment length(s) may be 53,567 bps INFO @ Sat, 11 Dec 2021 09:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.20_model.r WARNING @ Sat, 11 Dec 2021 09:11:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:11:34: #2 You may need to consider one of the other alternative d(s): 53,567 WARNING @ Sat, 11 Dec 2021 09:11:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:11:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:11:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:11:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689097/SRX8689097.20_summits.bed INFO @ Sat, 11 Dec 2021 09:11:53: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 2 millis CompletedMACS2peakCalling