Job ID = 14170926 SRX = SRX8689079 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: 00:00:01 Multiseed full-index search: 00:02:29 7841219 reads; of these: 7841219 (100.00%) were unpaired; of these: 320930 (4.09%) aligned 0 times 5563753 (70.96%) aligned exactly 1 time 1956536 (24.95%) aligned >1 times 95.91% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 537094 / 7520289 = 0.0714 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 09:06:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.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 09:06:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:15: 1000000 INFO @ Sat, 11 Dec 2021 09:06:24: 2000000 INFO @ Sat, 11 Dec 2021 09:06:32: 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 09:06:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.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 09:06:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:40: 4000000 INFO @ Sat, 11 Dec 2021 09:06:44: 1000000 INFO @ Sat, 11 Dec 2021 09:06:48: 5000000 INFO @ Sat, 11 Dec 2021 09:06:51: 2000000 INFO @ Sat, 11 Dec 2021 09:06:56: 6000000 INFO @ Sat, 11 Dec 2021 09:06:58: 3000000 INFO @ Sat, 11 Dec 2021 09:07:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:04: #1 total tags in treatment: 6983195 INFO @ Sat, 11 Dec 2021 09:07:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Sat, 11 Dec 2021 09:07:05: #1 tags after filtering in treatment: 6983031 INFO @ Sat, 11 Dec 2021 09:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:05: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:05: #2 looking for paired plus/minus strand peaks... 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 09:07:05: #2 number of paired peaks: 829 WARNING @ Sat, 11 Dec 2021 09:07:05: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:05: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:05: 4000000 INFO @ Sat, 11 Dec 2021 09:07:05: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:05: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:05: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:05: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:07:05: #2 alternative fragment length(s) may be 55,554 bps INFO @ Sat, 11 Dec 2021 09:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.05_model.r WARNING @ Sat, 11 Dec 2021 09:07:05: #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 09:07:05: #2 You may need to consider one of the other alternative d(s): 55,554 WARNING @ Sat, 11 Dec 2021 09:07:05: #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 09:07:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.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 09:07:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:12: 5000000 INFO @ Sat, 11 Dec 2021 09:07:15: 1000000 INFO @ Sat, 11 Dec 2021 09:07:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:07:20: 6000000 INFO @ Sat, 11 Dec 2021 09:07:23: 2000000 INFO @ Sat, 11 Dec 2021 09:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.05_summits.bed INFO @ Sat, 11 Dec 2021 09:07:27: Done! INFO @ Sat, 11 Dec 2021 09:07:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:28: #1 total tags in treatment: 6983195 INFO @ Sat, 11 Dec 2021 09:07:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (593 chroms): 3 millis pass2 - checking and writing primary data (2224 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:07:28: #1 tags after filtering in treatment: 6983031 INFO @ Sat, 11 Dec 2021 09:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:28: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:29: #2 number of paired peaks: 829 WARNING @ Sat, 11 Dec 2021 09:07:29: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:29: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:29: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:29: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:29: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:29: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:07:29: #2 alternative fragment length(s) may be 55,554 bps INFO @ Sat, 11 Dec 2021 09:07:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.10_model.r WARNING @ Sat, 11 Dec 2021 09:07:29: #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 09:07:29: #2 You may need to consider one of the other alternative d(s): 55,554 WARNING @ Sat, 11 Dec 2021 09:07:29: #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 09:07:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:30: 3000000 INFO @ Sat, 11 Dec 2021 09:07:37: 4000000 INFO @ Sat, 11 Dec 2021 09:07:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:07:44: 5000000 INFO @ Sat, 11 Dec 2021 09:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.10_summits.bed INFO @ Sat, 11 Dec 2021 09:07:51: Done! pass1 - making usageList (432 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:07:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:07:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:59: #1 total tags in treatment: 6983195 INFO @ Sat, 11 Dec 2021 09:07:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:59: #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 09:08:00: #1 tags after filtering in treatment: 6983031 INFO @ Sat, 11 Dec 2021 09:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:08:00: #1 finished! INFO @ Sat, 11 Dec 2021 09:08:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:08:00: #2 number of paired peaks: 829 WARNING @ Sat, 11 Dec 2021 09:08:00: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Sat, 11 Dec 2021 09:08:00: start model_add_line... INFO @ Sat, 11 Dec 2021 09:08:00: start X-correlation... INFO @ Sat, 11 Dec 2021 09:08:00: end of X-cor INFO @ Sat, 11 Dec 2021 09:08:00: #2 finished! INFO @ Sat, 11 Dec 2021 09:08:00: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:08:00: #2 alternative fragment length(s) may be 55,554 bps INFO @ Sat, 11 Dec 2021 09:08:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.20_model.r WARNING @ Sat, 11 Dec 2021 09:08:00: #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 09:08:00: #2 You may need to consider one of the other alternative d(s): 55,554 WARNING @ Sat, 11 Dec 2021 09:08:00: #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 09:08:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:08:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:08:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689079/SRX8689079.20_summits.bed INFO @ Sat, 11 Dec 2021 09:08:22: Done! pass1 - making usageList (182 chroms): 2 millis pass2 - checking and writing primary data (319 records, 4 fields): 23 millis CompletedMACS2peakCalling