Job ID = 14170855 SRX = SRX8689029 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: 00:02:15 7120373 reads; of these: 7120373 (100.00%) were unpaired; of these: 241263 (3.39%) aligned 0 times 4597029 (64.56%) aligned exactly 1 time 2282081 (32.05%) aligned >1 times 96.61% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 685884 / 6879110 = 0.0997 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 08:56:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.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 08:56:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:56:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:57:01: 1000000 INFO @ Sat, 11 Dec 2021 08:57:07: 2000000 INFO @ Sat, 11 Dec 2021 08:57:13: 3000000 INFO @ Sat, 11 Dec 2021 08:57:19: 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 08:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.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 08:57:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:57:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:57:25: 5000000 INFO @ Sat, 11 Dec 2021 08:57:31: 1000000 INFO @ Sat, 11 Dec 2021 08:57:33: 6000000 INFO @ Sat, 11 Dec 2021 08:57:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:57:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:57:34: #1 total tags in treatment: 6193226 INFO @ Sat, 11 Dec 2021 08:57:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:57:34: #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 08:57:34: #1 tags after filtering in treatment: 6193223 INFO @ Sat, 11 Dec 2021 08:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:57:34: #1 finished! INFO @ Sat, 11 Dec 2021 08:57:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:57:35: #2 number of paired peaks: 541 WARNING @ Sat, 11 Dec 2021 08:57:35: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 11 Dec 2021 08:57:35: start model_add_line... INFO @ Sat, 11 Dec 2021 08:57:35: start X-correlation... INFO @ Sat, 11 Dec 2021 08:57:35: end of X-cor INFO @ Sat, 11 Dec 2021 08:57:35: #2 finished! INFO @ Sat, 11 Dec 2021 08:57:35: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Dec 2021 08:57:35: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 11 Dec 2021 08:57:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.05_model.r WARNING @ Sat, 11 Dec 2021 08:57:35: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:57:35: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 11 Dec 2021 08:57:35: #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 08:57:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:57:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:57:38: 2000000 INFO @ Sat, 11 Dec 2021 08:57:44: 3000000 INFO @ Sat, 11 Dec 2021 08:57:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:57:50: 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 08:57:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.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 08:57:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:57:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:57:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:57:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:57:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.05_summits.bed INFO @ Sat, 11 Dec 2021 08:57:56: Done! pass1 - making usageList (520 chroms): 1 millis pass2 - checking and writing primary data (1424 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:57:56: 5000000 INFO @ Sat, 11 Dec 2021 08:58:01: 1000000 INFO @ Sat, 11 Dec 2021 08:58:04: 6000000 INFO @ Sat, 11 Dec 2021 08:58:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:58:05: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:58:05: #1 total tags in treatment: 6193226 INFO @ Sat, 11 Dec 2021 08:58:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:58:05: #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 08:58:05: #1 tags after filtering in treatment: 6193223 INFO @ Sat, 11 Dec 2021 08:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:58:05: #1 finished! INFO @ Sat, 11 Dec 2021 08:58:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:58:06: #2 number of paired peaks: 541 WARNING @ Sat, 11 Dec 2021 08:58:06: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 11 Dec 2021 08:58:06: start model_add_line... INFO @ Sat, 11 Dec 2021 08:58:06: start X-correlation... INFO @ Sat, 11 Dec 2021 08:58:06: end of X-cor INFO @ Sat, 11 Dec 2021 08:58:06: #2 finished! INFO @ Sat, 11 Dec 2021 08:58:06: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Dec 2021 08:58:06: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 11 Dec 2021 08:58:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.10_model.r WARNING @ Sat, 11 Dec 2021 08:58:06: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:58:06: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 11 Dec 2021 08:58:06: #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 08:58:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:58:08: 2000000 INFO @ Sat, 11 Dec 2021 08:58:14: 3000000 INFO @ Sat, 11 Dec 2021 08:58:20: 4000000 INFO @ Sat, 11 Dec 2021 08:58:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:58:26: 5000000 INFO @ Sat, 11 Dec 2021 08:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.10_summits.bed INFO @ Sat, 11 Dec 2021 08:58:27: Done! pass1 - making usageList (288 chroms): 1 millis pass2 - checking and writing primary data (603 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:58:32: 6000000 INFO @ Sat, 11 Dec 2021 08:58:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:58:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:58:33: #1 total tags in treatment: 6193226 INFO @ Sat, 11 Dec 2021 08:58:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:58:33: #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 08:58:34: #1 tags after filtering in treatment: 6193223 INFO @ Sat, 11 Dec 2021 08:58:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:58:34: #1 finished! INFO @ Sat, 11 Dec 2021 08:58:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:58:34: #2 number of paired peaks: 541 WARNING @ Sat, 11 Dec 2021 08:58:34: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 11 Dec 2021 08:58:34: start model_add_line... INFO @ Sat, 11 Dec 2021 08:58:34: start X-correlation... INFO @ Sat, 11 Dec 2021 08:58:34: end of X-cor INFO @ Sat, 11 Dec 2021 08:58:34: #2 finished! INFO @ Sat, 11 Dec 2021 08:58:34: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Dec 2021 08:58:34: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 11 Dec 2021 08:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.20_model.r WARNING @ Sat, 11 Dec 2021 08:58:34: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:58:34: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 11 Dec 2021 08:58:34: #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 08:58:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:58:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:58:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689029/SRX8689029.20_summits.bed INFO @ Sat, 11 Dec 2021 08:58:55: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 6 millis CompletedMACS2peakCalling