Job ID = 14170756 SRX = SRX8689104 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: 00:05:41 19125540 reads; of these: 19125540 (100.00%) were unpaired; of these: 588073 (3.07%) aligned 0 times 13345014 (69.78%) aligned exactly 1 time 5192453 (27.15%) aligned >1 times 96.93% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2262896 / 18537467 = 0.1221 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 08:34:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.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 08:34:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:34:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:34:51: 1000000 INFO @ Sat, 11 Dec 2021 08:34:57: 2000000 INFO @ Sat, 11 Dec 2021 08:35:02: 3000000 INFO @ Sat, 11 Dec 2021 08:35:08: 4000000 INFO @ Sat, 11 Dec 2021 08:35:13: 5000000 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 08:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.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 08:35:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:35:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:35:19: 6000000 INFO @ Sat, 11 Dec 2021 08:35:21: 1000000 INFO @ Sat, 11 Dec 2021 08:35:24: 7000000 INFO @ Sat, 11 Dec 2021 08:35:27: 2000000 INFO @ Sat, 11 Dec 2021 08:35:30: 8000000 INFO @ Sat, 11 Dec 2021 08:35:33: 3000000 INFO @ Sat, 11 Dec 2021 08:35:36: 9000000 INFO @ Sat, 11 Dec 2021 08:35:39: 4000000 INFO @ Sat, 11 Dec 2021 08:35:42: 10000000 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 08:35:44: 5000000 INFO @ Sat, 11 Dec 2021 08:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.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 08:35:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:35:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:35:47: 11000000 INFO @ Sat, 11 Dec 2021 08:35:50: 6000000 INFO @ Sat, 11 Dec 2021 08:35:51: 1000000 INFO @ Sat, 11 Dec 2021 08:35:53: 12000000 INFO @ Sat, 11 Dec 2021 08:35:56: 7000000 INFO @ Sat, 11 Dec 2021 08:35:57: 2000000 INFO @ Sat, 11 Dec 2021 08:35:59: 13000000 INFO @ Sat, 11 Dec 2021 08:36:01: 8000000 INFO @ Sat, 11 Dec 2021 08:36:03: 3000000 INFO @ Sat, 11 Dec 2021 08:36:05: 14000000 INFO @ Sat, 11 Dec 2021 08:36:07: 9000000 INFO @ Sat, 11 Dec 2021 08:36:08: 4000000 INFO @ Sat, 11 Dec 2021 08:36:11: 15000000 INFO @ Sat, 11 Dec 2021 08:36:13: 10000000 INFO @ Sat, 11 Dec 2021 08:36:14: 5000000 INFO @ Sat, 11 Dec 2021 08:36:17: 16000000 INFO @ Sat, 11 Dec 2021 08:36:18: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:36:18: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:36:18: #1 total tags in treatment: 16274571 INFO @ Sat, 11 Dec 2021 08:36:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:36:18: #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 08:36:18: 11000000 INFO @ Sat, 11 Dec 2021 08:36:19: #1 tags after filtering in treatment: 16274503 INFO @ Sat, 11 Dec 2021 08:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:36:19: #1 finished! INFO @ Sat, 11 Dec 2021 08:36:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:36:20: 6000000 INFO @ Sat, 11 Dec 2021 08:36:20: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 08:36:20: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 08:36:20: start model_add_line... INFO @ Sat, 11 Dec 2021 08:36:20: start X-correlation... INFO @ Sat, 11 Dec 2021 08:36:20: end of X-cor INFO @ Sat, 11 Dec 2021 08:36:20: #2 finished! INFO @ Sat, 11 Dec 2021 08:36:20: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 08:36:20: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sat, 11 Dec 2021 08:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.05_model.r WARNING @ Sat, 11 Dec 2021 08:36:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:36:20: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sat, 11 Dec 2021 08:36:20: #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 08:36:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:36:24: 12000000 INFO @ Sat, 11 Dec 2021 08:36:25: 7000000 INFO @ Sat, 11 Dec 2021 08:36:30: 13000000 INFO @ Sat, 11 Dec 2021 08:36:31: 8000000 INFO @ Sat, 11 Dec 2021 08:36:36: 14000000 INFO @ Sat, 11 Dec 2021 08:36:37: 9000000 INFO @ Sat, 11 Dec 2021 08:36:42: 15000000 INFO @ Sat, 11 Dec 2021 08:36:42: 10000000 INFO @ Sat, 11 Dec 2021 08:36:47: 16000000 INFO @ Sat, 11 Dec 2021 08:36:48: 11000000 INFO @ Sat, 11 Dec 2021 08:36:49: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:36:49: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:36:49: #1 total tags in treatment: 16274571 INFO @ Sat, 11 Dec 2021 08:36:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:36:49: #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 08:36:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:36:50: #1 tags after filtering in treatment: 16274503 INFO @ Sat, 11 Dec 2021 08:36:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:36:50: #1 finished! INFO @ Sat, 11 Dec 2021 08:36:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:36:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:36:51: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 08:36:51: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 08:36:51: start model_add_line... INFO @ Sat, 11 Dec 2021 08:36:51: start X-correlation... INFO @ Sat, 11 Dec 2021 08:36:51: end of X-cor INFO @ Sat, 11 Dec 2021 08:36:51: #2 finished! INFO @ Sat, 11 Dec 2021 08:36:51: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 08:36:51: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sat, 11 Dec 2021 08:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.10_model.r WARNING @ Sat, 11 Dec 2021 08:36:51: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:36:51: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sat, 11 Dec 2021 08:36:51: #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 08:36:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:36:53: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:36:59: 13000000 INFO @ Sat, 11 Dec 2021 08:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.05_summits.bed INFO @ Sat, 11 Dec 2021 08:37:04: Done! pass1 - making usageList (700 chroms): 2 millis pass2 - checking and writing primary data (3274 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:37:05: 14000000 INFO @ Sat, 11 Dec 2021 08:37:10: 15000000 INFO @ Sat, 11 Dec 2021 08:37:16: 16000000 INFO @ Sat, 11 Dec 2021 08:37:18: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:37:18: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:37:18: #1 total tags in treatment: 16274571 INFO @ Sat, 11 Dec 2021 08:37:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:37:18: #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 08:37:18: #1 tags after filtering in treatment: 16274503 INFO @ Sat, 11 Dec 2021 08:37:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:37:18: #1 finished! INFO @ Sat, 11 Dec 2021 08:37:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:37:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:37:19: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 08:37:19: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 08:37:19: start model_add_line... INFO @ Sat, 11 Dec 2021 08:37:19: start X-correlation... INFO @ Sat, 11 Dec 2021 08:37:19: end of X-cor INFO @ Sat, 11 Dec 2021 08:37:19: #2 finished! INFO @ Sat, 11 Dec 2021 08:37:19: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 08:37:19: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sat, 11 Dec 2021 08:37:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.20_model.r WARNING @ Sat, 11 Dec 2021 08:37:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:37:20: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sat, 11 Dec 2021 08:37:20: #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 08:37:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:37:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:37:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.10_summits.bed INFO @ Sat, 11 Dec 2021 08:37:35: Done! pass1 - making usageList (594 chroms): 1 millis pass2 - checking and writing primary data (2330 records, 4 fields): 250 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:37:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:38:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:38:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:38:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689104/SRX8689104.20_summits.bed INFO @ Sat, 11 Dec 2021 08:38:04: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (876 records, 4 fields): 12 millis CompletedMACS2peakCalling