Job ID = 14170970 SRX = SRX8689098 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: 00:01:44 5860406 reads; of these: 5860406 (100.00%) were unpaired; of these: 183057 (3.12%) aligned 0 times 4504544 (76.86%) aligned exactly 1 time 1172805 (20.01%) aligned >1 times 96.88% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 328334 / 5677349 = 0.0578 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 09:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.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 09:10:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:10:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:10:59: 1000000 INFO @ Sat, 11 Dec 2021 09:11:05: 2000000 INFO @ Sat, 11 Dec 2021 09:11:10: 3000000 INFO @ Sat, 11 Dec 2021 09:11:16: 4000000 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 09:11:22: 5000000 INFO @ Sat, 11 Dec 2021 09:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.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 09:11:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:11:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:11:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:11:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:11:24: #1 total tags in treatment: 5349015 INFO @ Sat, 11 Dec 2021 09:11:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:11:24: #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 09:11:25: #1 tags after filtering in treatment: 5348997 INFO @ Sat, 11 Dec 2021 09:11:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:11:25: #1 finished! INFO @ Sat, 11 Dec 2021 09:11:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:11:25: #2 number of paired peaks: 185 WARNING @ Sat, 11 Dec 2021 09:11:25: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 11 Dec 2021 09:11:25: start model_add_line... INFO @ Sat, 11 Dec 2021 09:11:25: start X-correlation... INFO @ Sat, 11 Dec 2021 09:11:25: end of X-cor INFO @ Sat, 11 Dec 2021 09:11:25: #2 finished! INFO @ Sat, 11 Dec 2021 09:11:25: #2 predicted fragment length is 65 bps INFO @ Sat, 11 Dec 2021 09:11:25: #2 alternative fragment length(s) may be 65 bps INFO @ Sat, 11 Dec 2021 09:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.05_model.r WARNING @ Sat, 11 Dec 2021 09:11:25: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:11:25: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Sat, 11 Dec 2021 09:11:25: #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 09:11:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:11:30: 1000000 INFO @ Sat, 11 Dec 2021 09:11:36: 2000000 INFO @ Sat, 11 Dec 2021 09:11:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:11:42: 3000000 INFO @ Sat, 11 Dec 2021 09:11:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.05_summits.bed INFO @ Sat, 11 Dec 2021 09:11:42: Done! pass1 - making usageList (186 chroms): 2 millis pass2 - checking and writing primary data (421 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:11:48: 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 09:11:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.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 09:11:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:11:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:11:55: 5000000 INFO @ Sat, 11 Dec 2021 09:11:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:11:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:11:57: #1 total tags in treatment: 5349015 INFO @ Sat, 11 Dec 2021 09:11:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:11:57: #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 09:11:58: #1 tags after filtering in treatment: 5348997 INFO @ Sat, 11 Dec 2021 09:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:11:58: #1 finished! INFO @ Sat, 11 Dec 2021 09:11:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:11:58: #2 number of paired peaks: 185 WARNING @ Sat, 11 Dec 2021 09:11:58: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 11 Dec 2021 09:11:58: start model_add_line... INFO @ Sat, 11 Dec 2021 09:11:59: start X-correlation... INFO @ Sat, 11 Dec 2021 09:11:59: end of X-cor INFO @ Sat, 11 Dec 2021 09:11:59: #2 finished! INFO @ Sat, 11 Dec 2021 09:11:59: #2 predicted fragment length is 65 bps INFO @ Sat, 11 Dec 2021 09:11:59: #2 alternative fragment length(s) may be 65 bps INFO @ Sat, 11 Dec 2021 09:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.10_model.r WARNING @ Sat, 11 Dec 2021 09:11:59: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:11:59: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Sat, 11 Dec 2021 09:11:59: #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 09:11:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:12:00: 1000000 INFO @ Sat, 11 Dec 2021 09:12:05: 2000000 INFO @ Sat, 11 Dec 2021 09:12:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:12:11: 3000000 INFO @ Sat, 11 Dec 2021 09:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.10_summits.bed INFO @ Sat, 11 Dec 2021 09:12:15: Done! pass1 - making usageList (108 chroms): 2 millis pass2 - checking and writing primary data (247 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:12:16: 4000000 INFO @ Sat, 11 Dec 2021 09:12:22: 5000000 INFO @ Sat, 11 Dec 2021 09:12:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:12:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:12:24: #1 total tags in treatment: 5349015 INFO @ Sat, 11 Dec 2021 09:12:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:12:24: #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 09:12:25: #1 tags after filtering in treatment: 5348997 INFO @ Sat, 11 Dec 2021 09:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:12:25: #1 finished! INFO @ Sat, 11 Dec 2021 09:12:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:12:25: #2 number of paired peaks: 185 WARNING @ Sat, 11 Dec 2021 09:12:25: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 11 Dec 2021 09:12:25: start model_add_line... INFO @ Sat, 11 Dec 2021 09:12:26: start X-correlation... INFO @ Sat, 11 Dec 2021 09:12:26: end of X-cor INFO @ Sat, 11 Dec 2021 09:12:26: #2 finished! INFO @ Sat, 11 Dec 2021 09:12:26: #2 predicted fragment length is 65 bps INFO @ Sat, 11 Dec 2021 09:12:26: #2 alternative fragment length(s) may be 65 bps INFO @ Sat, 11 Dec 2021 09:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.20_model.r WARNING @ Sat, 11 Dec 2021 09:12:26: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:12:26: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Sat, 11 Dec 2021 09:12:26: #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 09:12:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:12:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:12:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689098/SRX8689098.20_summits.bed INFO @ Sat, 11 Dec 2021 09:12:43: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。