Job ID = 14170793 SRX = SRX8689009 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: 00:06:36 20863471 reads; of these: 20863471 (100.00%) were unpaired; of these: 688541 (3.30%) aligned 0 times 13676350 (65.55%) aligned exactly 1 time 6498580 (31.15%) aligned >1 times 96.70% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 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 12 files... [bam_rmdupse_core] 2928741 / 20174930 = 0.1452 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 08:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.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 08:55:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:55:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:55:45: 1000000 INFO @ Sat, 11 Dec 2021 08:55:51: 2000000 INFO @ Sat, 11 Dec 2021 08:55:57: 3000000 INFO @ Sat, 11 Dec 2021 08:56:03: 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 08:56:09: 5000000 INFO @ Sat, 11 Dec 2021 08:56:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.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 08:56:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:56:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:56:15: 1000000 INFO @ Sat, 11 Dec 2021 08:56:15: 6000000 INFO @ Sat, 11 Dec 2021 08:56:21: 2000000 INFO @ Sat, 11 Dec 2021 08:56:21: 7000000 INFO @ Sat, 11 Dec 2021 08:56:26: 3000000 INFO @ Sat, 11 Dec 2021 08:56:27: 8000000 INFO @ Sat, 11 Dec 2021 08:56:32: 4000000 INFO @ Sat, 11 Dec 2021 08:56:34: 9000000 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 08:56:38: 5000000 INFO @ Sat, 11 Dec 2021 08:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.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 08:56:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:56:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:56:40: 10000000 INFO @ Sat, 11 Dec 2021 08:56:44: 6000000 INFO @ Sat, 11 Dec 2021 08:56:45: 1000000 INFO @ Sat, 11 Dec 2021 08:56:46: 11000000 INFO @ Sat, 11 Dec 2021 08:56:50: 7000000 INFO @ Sat, 11 Dec 2021 08:56:52: 2000000 INFO @ Sat, 11 Dec 2021 08:56:53: 12000000 INFO @ Sat, 11 Dec 2021 08:56:56: 8000000 INFO @ Sat, 11 Dec 2021 08:56:59: 3000000 INFO @ Sat, 11 Dec 2021 08:56:59: 13000000 INFO @ Sat, 11 Dec 2021 08:57:01: 9000000 INFO @ Sat, 11 Dec 2021 08:57:05: 14000000 INFO @ Sat, 11 Dec 2021 08:57:06: 4000000 INFO @ Sat, 11 Dec 2021 08:57:07: 10000000 INFO @ Sat, 11 Dec 2021 08:57:12: 15000000 INFO @ Sat, 11 Dec 2021 08:57:12: 5000000 INFO @ Sat, 11 Dec 2021 08:57:13: 11000000 INFO @ Sat, 11 Dec 2021 08:57:19: 16000000 INFO @ Sat, 11 Dec 2021 08:57:19: 12000000 INFO @ Sat, 11 Dec 2021 08:57:19: 6000000 INFO @ Sat, 11 Dec 2021 08:57:25: 13000000 INFO @ Sat, 11 Dec 2021 08:57:25: 17000000 INFO @ Sat, 11 Dec 2021 08:57:26: 7000000 INFO @ Sat, 11 Dec 2021 08:57:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:57:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:57:27: #1 total tags in treatment: 17246189 INFO @ Sat, 11 Dec 2021 08:57:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:57:27: #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 08:57:27: #1 tags after filtering in treatment: 17246189 INFO @ Sat, 11 Dec 2021 08:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:57:27: #1 finished! INFO @ Sat, 11 Dec 2021 08:57:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:57:29: #2 number of paired peaks: 370 WARNING @ Sat, 11 Dec 2021 08:57:29: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sat, 11 Dec 2021 08:57:29: start model_add_line... INFO @ Sat, 11 Dec 2021 08:57:29: start X-correlation... INFO @ Sat, 11 Dec 2021 08:57:29: end of X-cor INFO @ Sat, 11 Dec 2021 08:57:29: #2 finished! INFO @ Sat, 11 Dec 2021 08:57:29: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 08:57:29: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 08:57:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.05_model.r WARNING @ Sat, 11 Dec 2021 08:57:29: #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 08:57:29: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 08:57:29: #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 08:57:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:57:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:57:31: 14000000 INFO @ Sat, 11 Dec 2021 08:57:32: 8000000 INFO @ Sat, 11 Dec 2021 08:57:37: 15000000 INFO @ Sat, 11 Dec 2021 08:57:39: 9000000 INFO @ Sat, 11 Dec 2021 08:57:43: 16000000 INFO @ Sat, 11 Dec 2021 08:57:45: 10000000 INFO @ Sat, 11 Dec 2021 08:57:49: 17000000 INFO @ Sat, 11 Dec 2021 08:57:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:57:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:57:51: #1 total tags in treatment: 17246189 INFO @ Sat, 11 Dec 2021 08:57:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:57:51: #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 08:57:51: #1 tags after filtering in treatment: 17246189 INFO @ Sat, 11 Dec 2021 08:57:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:57:51: #1 finished! INFO @ Sat, 11 Dec 2021 08:57:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:57:51: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:57:52: #2 number of paired peaks: 370 WARNING @ Sat, 11 Dec 2021 08:57:52: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sat, 11 Dec 2021 08:57:52: start model_add_line... INFO @ Sat, 11 Dec 2021 08:57:52: start X-correlation... INFO @ Sat, 11 Dec 2021 08:57:52: end of X-cor INFO @ Sat, 11 Dec 2021 08:57:52: #2 finished! INFO @ Sat, 11 Dec 2021 08:57:52: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 08:57:52: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 08:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.10_model.r WARNING @ Sat, 11 Dec 2021 08:57:52: #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 08:57:52: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 08:57:52: #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 08:57:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:57:58: 12000000 INFO @ Sat, 11 Dec 2021 08:58:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:58:04: 13000000 INFO @ Sat, 11 Dec 2021 08:58:10: 14000000 INFO @ Sat, 11 Dec 2021 08:58:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:58:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:58:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.05_summits.bed INFO @ Sat, 11 Dec 2021 08:58:15: Done! pass1 - making usageList (850 chroms): 2 millis pass2 - checking and writing primary data (3653 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:58:16: 15000000 INFO @ Sat, 11 Dec 2021 08:58:22: 16000000 INFO @ Sat, 11 Dec 2021 08:58:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:58:28: 17000000 INFO @ Sat, 11 Dec 2021 08:58:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:58:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:58:30: #1 total tags in treatment: 17246189 INFO @ Sat, 11 Dec 2021 08:58:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:58:30: #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 08:58:30: #1 tags after filtering in treatment: 17246189 INFO @ Sat, 11 Dec 2021 08:58:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:58:30: #1 finished! INFO @ Sat, 11 Dec 2021 08:58:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:58:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:58:32: #2 number of paired peaks: 370 WARNING @ Sat, 11 Dec 2021 08:58:32: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sat, 11 Dec 2021 08:58:32: start model_add_line... INFO @ Sat, 11 Dec 2021 08:58:32: start X-correlation... INFO @ Sat, 11 Dec 2021 08:58:32: end of X-cor INFO @ Sat, 11 Dec 2021 08:58:32: #2 finished! INFO @ Sat, 11 Dec 2021 08:58:32: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 08:58:32: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 08:58:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.20_model.r WARNING @ Sat, 11 Dec 2021 08:58:32: #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 08:58:32: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 08:58:32: #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 08:58:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.10_summits.bed INFO @ Sat, 11 Dec 2021 08:58:37: Done! pass1 - making usageList (532 chroms): 1 millis pass2 - checking and writing primary data (1615 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:59:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689009/SRX8689009.20_summits.bed INFO @ Sat, 11 Dec 2021 08:59:17: Done! pass1 - making usageList (289 chroms): 1 millis pass2 - checking and writing primary data (579 records, 4 fields): 9 millis CompletedMACS2peakCalling