Job ID = 14170781 SRX = SRX8689006 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: 00:05:13 18158016 reads; of these: 18158016 (100.00%) were unpaired; of these: 575727 (3.17%) aligned 0 times 12542757 (69.08%) aligned exactly 1 time 5039532 (27.75%) aligned >1 times 96.83% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 2308503 / 17582289 = 0.1313 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 08:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.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 08:46:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:46:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:46:33: 1000000 INFO @ Sat, 11 Dec 2021 08:46:38: 2000000 INFO @ Sat, 11 Dec 2021 08:46:43: 3000000 INFO @ Sat, 11 Dec 2021 08:46:48: 4000000 INFO @ Sat, 11 Dec 2021 08:46:53: 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 08:46:58: 6000000 INFO @ Sat, 11 Dec 2021 08:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.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 08:46:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:46:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:47:03: 7000000 INFO @ Sat, 11 Dec 2021 08:47:04: 1000000 INFO @ Sat, 11 Dec 2021 08:47:08: 8000000 INFO @ Sat, 11 Dec 2021 08:47:09: 2000000 INFO @ Sat, 11 Dec 2021 08:47:12: 9000000 INFO @ Sat, 11 Dec 2021 08:47:14: 3000000 INFO @ Sat, 11 Dec 2021 08:47:17: 10000000 INFO @ Sat, 11 Dec 2021 08:47:19: 4000000 INFO @ Sat, 11 Dec 2021 08:47:22: 11000000 INFO @ Sat, 11 Dec 2021 08:47:24: 5000000 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 08:47:28: 12000000 INFO @ Sat, 11 Dec 2021 08:47:29: 6000000 INFO @ Sat, 11 Dec 2021 08:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.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 08:47:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:47:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:47:33: 13000000 INFO @ Sat, 11 Dec 2021 08:47:34: 7000000 INFO @ Sat, 11 Dec 2021 08:47:34: 1000000 INFO @ Sat, 11 Dec 2021 08:47:38: 14000000 INFO @ Sat, 11 Dec 2021 08:47:39: 8000000 INFO @ Sat, 11 Dec 2021 08:47:39: 2000000 INFO @ Sat, 11 Dec 2021 08:47:43: 15000000 INFO @ Sat, 11 Dec 2021 08:47:44: 9000000 INFO @ Sat, 11 Dec 2021 08:47:44: 3000000 INFO @ Sat, 11 Dec 2021 08:47:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:47:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:47:44: #1 total tags in treatment: 15273786 INFO @ Sat, 11 Dec 2021 08:47:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:47:44: #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 08:47:45: #1 tags after filtering in treatment: 15273732 INFO @ Sat, 11 Dec 2021 08:47:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:47:45: #1 finished! INFO @ Sat, 11 Dec 2021 08:47:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:47:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:47:46: #2 number of paired peaks: 754 WARNING @ Sat, 11 Dec 2021 08:47:46: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Sat, 11 Dec 2021 08:47:46: start model_add_line... INFO @ Sat, 11 Dec 2021 08:47:46: start X-correlation... INFO @ Sat, 11 Dec 2021 08:47:46: end of X-cor INFO @ Sat, 11 Dec 2021 08:47:46: #2 finished! INFO @ Sat, 11 Dec 2021 08:47:46: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 08:47:46: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sat, 11 Dec 2021 08:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.05_model.r WARNING @ Sat, 11 Dec 2021 08:47:46: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:47:46: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sat, 11 Dec 2021 08:47:46: #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 08:47:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:47:49: 10000000 INFO @ Sat, 11 Dec 2021 08:47:49: 4000000 INFO @ Sat, 11 Dec 2021 08:47:54: 11000000 INFO @ Sat, 11 Dec 2021 08:47:54: 5000000 INFO @ Sat, 11 Dec 2021 08:47:59: 12000000 INFO @ Sat, 11 Dec 2021 08:47:59: 6000000 INFO @ Sat, 11 Dec 2021 08:48:04: 13000000 INFO @ Sat, 11 Dec 2021 08:48:04: 7000000 INFO @ Sat, 11 Dec 2021 08:48:09: 14000000 INFO @ Sat, 11 Dec 2021 08:48:09: 8000000 INFO @ Sat, 11 Dec 2021 08:48:14: 9000000 INFO @ Sat, 11 Dec 2021 08:48:14: 15000000 INFO @ Sat, 11 Dec 2021 08:48:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:48:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:48:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:48:15: #1 total tags in treatment: 15273786 INFO @ Sat, 11 Dec 2021 08:48:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:48:15: #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 08:48:16: #1 tags after filtering in treatment: 15273732 INFO @ Sat, 11 Dec 2021 08:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:48:16: #1 finished! INFO @ Sat, 11 Dec 2021 08:48:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:48:17: #2 number of paired peaks: 754 WARNING @ Sat, 11 Dec 2021 08:48:17: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Sat, 11 Dec 2021 08:48:17: start model_add_line... INFO @ Sat, 11 Dec 2021 08:48:17: start X-correlation... INFO @ Sat, 11 Dec 2021 08:48:17: end of X-cor INFO @ Sat, 11 Dec 2021 08:48:17: #2 finished! INFO @ Sat, 11 Dec 2021 08:48:17: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 08:48:17: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sat, 11 Dec 2021 08:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.10_model.r WARNING @ Sat, 11 Dec 2021 08:48:17: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:48:17: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sat, 11 Dec 2021 08:48:17: #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 08:48:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:48:19: 10000000 INFO @ Sat, 11 Dec 2021 08:48:23: 11000000 INFO @ Sat, 11 Dec 2021 08:48:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:48:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:48:29: 12000000 INFO @ Sat, 11 Dec 2021 08:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.05_summits.bed INFO @ Sat, 11 Dec 2021 08:48:29: Done! pass1 - making usageList (703 chroms): 2 millis pass2 - checking and writing primary data (3433 records, 4 fields): 104 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:48:33: 13000000 INFO @ Sat, 11 Dec 2021 08:48:38: 14000000 INFO @ Sat, 11 Dec 2021 08:48:43: 15000000 INFO @ Sat, 11 Dec 2021 08:48:45: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:48:45: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:48:45: #1 total tags in treatment: 15273786 INFO @ Sat, 11 Dec 2021 08:48:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:48:45: #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 08:48:45: #1 tags after filtering in treatment: 15273732 INFO @ Sat, 11 Dec 2021 08:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:48:45: #1 finished! INFO @ Sat, 11 Dec 2021 08:48:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:48:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:48:46: #2 number of paired peaks: 754 WARNING @ Sat, 11 Dec 2021 08:48:46: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Sat, 11 Dec 2021 08:48:46: start model_add_line... INFO @ Sat, 11 Dec 2021 08:48:46: start X-correlation... INFO @ Sat, 11 Dec 2021 08:48:46: end of X-cor INFO @ Sat, 11 Dec 2021 08:48:46: #2 finished! INFO @ Sat, 11 Dec 2021 08:48:46: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 08:48:46: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sat, 11 Dec 2021 08:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.20_model.r WARNING @ Sat, 11 Dec 2021 08:48:46: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:48:46: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sat, 11 Dec 2021 08:48:46: #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 08:48:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.10_summits.bed INFO @ Sat, 11 Dec 2021 08:48:59: Done! pass1 - making usageList (590 chroms): 2 millis pass2 - checking and writing primary data (2058 records, 4 fields): 84 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:49:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:49:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689006/SRX8689006.20_summits.bed INFO @ Sat, 11 Dec 2021 08:49:28: Done! pass1 - making usageList (299 chroms): 1 millis pass2 - checking and writing primary data (751 records, 4 fields): 31 millis CompletedMACS2peakCalling