Job ID = 14169121 SRX = SRX8688995 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: 00:05:45 20466163 reads; of these: 20466163 (100.00%) were unpaired; of these: 1234187 (6.03%) aligned 0 times 14057149 (68.68%) aligned exactly 1 time 5174827 (25.28%) aligned >1 times 93.97% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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] 2510311 / 19231976 = 0.1305 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 00:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.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 00:05:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:05:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:05:56: 1000000 INFO @ Sat, 11 Dec 2021 00:06:02: 2000000 INFO @ Sat, 11 Dec 2021 00:06:08: 3000000 INFO @ Sat, 11 Dec 2021 00:06:14: 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 00:06:20: 5000000 INFO @ Sat, 11 Dec 2021 00:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.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 00:06:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:06:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:06:27: 1000000 INFO @ Sat, 11 Dec 2021 00:06:27: 6000000 INFO @ Sat, 11 Dec 2021 00:06:33: 7000000 INFO @ Sat, 11 Dec 2021 00:06:34: 2000000 INFO @ Sat, 11 Dec 2021 00:06:40: 8000000 INFO @ Sat, 11 Dec 2021 00:06:40: 3000000 INFO @ Sat, 11 Dec 2021 00:06:47: 9000000 INFO @ Sat, 11 Dec 2021 00:06:47: 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 00:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.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 00:06:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:06:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:06:53: 10000000 INFO @ Sat, 11 Dec 2021 00:06:54: 5000000 INFO @ Sat, 11 Dec 2021 00:06:58: 1000000 INFO @ Sat, 11 Dec 2021 00:07:00: 11000000 INFO @ Sat, 11 Dec 2021 00:07:00: 6000000 INFO @ Sat, 11 Dec 2021 00:07:05: 2000000 INFO @ Sat, 11 Dec 2021 00:07:06: 12000000 INFO @ Sat, 11 Dec 2021 00:07:07: 7000000 INFO @ Sat, 11 Dec 2021 00:07:12: 3000000 INFO @ Sat, 11 Dec 2021 00:07:13: 13000000 INFO @ Sat, 11 Dec 2021 00:07:14: 8000000 INFO @ Sat, 11 Dec 2021 00:07:18: 4000000 INFO @ Sat, 11 Dec 2021 00:07:20: 14000000 INFO @ Sat, 11 Dec 2021 00:07:21: 9000000 INFO @ Sat, 11 Dec 2021 00:07:25: 5000000 INFO @ Sat, 11 Dec 2021 00:07:27: 15000000 INFO @ Sat, 11 Dec 2021 00:07:27: 10000000 INFO @ Sat, 11 Dec 2021 00:07:31: 6000000 INFO @ Sat, 11 Dec 2021 00:07:33: 16000000 INFO @ Sat, 11 Dec 2021 00:07:34: 11000000 INFO @ Sat, 11 Dec 2021 00:07:38: 7000000 INFO @ Sat, 11 Dec 2021 00:07:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:07:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:07:38: #1 total tags in treatment: 16721665 INFO @ Sat, 11 Dec 2021 00:07:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:07:38: #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 00:07:39: #1 tags after filtering in treatment: 16721665 INFO @ Sat, 11 Dec 2021 00:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:07:39: #1 finished! INFO @ Sat, 11 Dec 2021 00:07:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:07:40: #2 number of paired peaks: 188 WARNING @ Sat, 11 Dec 2021 00:07:40: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sat, 11 Dec 2021 00:07:40: start model_add_line... INFO @ Sat, 11 Dec 2021 00:07:40: start X-correlation... INFO @ Sat, 11 Dec 2021 00:07:40: end of X-cor INFO @ Sat, 11 Dec 2021 00:07:40: #2 finished! INFO @ Sat, 11 Dec 2021 00:07:40: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 00:07:40: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 11 Dec 2021 00:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.05_model.r WARNING @ Sat, 11 Dec 2021 00:07:40: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:07:40: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 11 Dec 2021 00:07:40: #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 00:07:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:07:41: 12000000 INFO @ Sat, 11 Dec 2021 00:07:45: 8000000 INFO @ Sat, 11 Dec 2021 00:07:48: 13000000 INFO @ Sat, 11 Dec 2021 00:07:51: 9000000 INFO @ Sat, 11 Dec 2021 00:07:55: 14000000 INFO @ Sat, 11 Dec 2021 00:07:57: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:08:02: 15000000 INFO @ Sat, 11 Dec 2021 00:08:04: 11000000 INFO @ Sat, 11 Dec 2021 00:08:09: 16000000 INFO @ Sat, 11 Dec 2021 00:08:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:08:10: 12000000 INFO @ Sat, 11 Dec 2021 00:08:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:08:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:08:14: #1 total tags in treatment: 16721665 INFO @ Sat, 11 Dec 2021 00:08:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:08:14: #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 00:08:14: #1 tags after filtering in treatment: 16721665 INFO @ Sat, 11 Dec 2021 00:08:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:08:14: #1 finished! INFO @ Sat, 11 Dec 2021 00:08:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:08:15: #2 number of paired peaks: 188 WARNING @ Sat, 11 Dec 2021 00:08:15: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sat, 11 Dec 2021 00:08:15: start model_add_line... INFO @ Sat, 11 Dec 2021 00:08:15: start X-correlation... INFO @ Sat, 11 Dec 2021 00:08:15: end of X-cor INFO @ Sat, 11 Dec 2021 00:08:15: #2 finished! INFO @ Sat, 11 Dec 2021 00:08:15: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 00:08:15: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 11 Dec 2021 00:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.10_model.r WARNING @ Sat, 11 Dec 2021 00:08:15: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:08:15: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 11 Dec 2021 00:08:15: #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 00:08:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:08:17: 13000000 INFO @ Sat, 11 Dec 2021 00:08:23: 14000000 INFO @ Sat, 11 Dec 2021 00:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.05_summits.bed INFO @ Sat, 11 Dec 2021 00:08:24: Done! pass1 - making usageList (573 chroms): 1 millis pass2 - checking and writing primary data (2441 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:08:30: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:08:36: 16000000 INFO @ Sat, 11 Dec 2021 00:08:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 00:08:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 00:08:41: #1 total tags in treatment: 16721665 INFO @ Sat, 11 Dec 2021 00:08:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:08:41: #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 00:08:41: #1 tags after filtering in treatment: 16721665 INFO @ Sat, 11 Dec 2021 00:08:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 00:08:41: #1 finished! INFO @ Sat, 11 Dec 2021 00:08:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:08:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:08:43: #2 number of paired peaks: 188 WARNING @ Sat, 11 Dec 2021 00:08:43: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Sat, 11 Dec 2021 00:08:43: start model_add_line... INFO @ Sat, 11 Dec 2021 00:08:43: start X-correlation... INFO @ Sat, 11 Dec 2021 00:08:43: end of X-cor INFO @ Sat, 11 Dec 2021 00:08:43: #2 finished! INFO @ Sat, 11 Dec 2021 00:08:43: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 00:08:43: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 11 Dec 2021 00:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.20_model.r WARNING @ Sat, 11 Dec 2021 00:08:43: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:08:43: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 11 Dec 2021 00:08:43: #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 00:08:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:08:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:09:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:09:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.10_summits.bed INFO @ Sat, 11 Dec 2021 00:09:00: Done! pass1 - making usageList (388 chroms): 1 millis pass2 - checking and writing primary data (1106 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:09:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:09:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688995/SRX8688995.20_summits.bed INFO @ Sat, 11 Dec 2021 00:09:28: Done! pass1 - making usageList (174 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 6 millis CompletedMACS2peakCalling