Job ID = 14172510 SRX = SRX10089753 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:11 25352395 reads; of these: 25352395 (100.00%) were unpaired; of these: 2544624 (10.04%) aligned 0 times 17695357 (69.80%) aligned exactly 1 time 5112414 (20.17%) aligned >1 times 89.96% overall alignment rate Time searching: 00:06:12 Overall time: 00:06:12 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] 3517668 / 22807771 = 0.1542 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 15:56:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.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 15:56:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:56:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:56:34: 1000000 INFO @ Sat, 11 Dec 2021 15:56:42: 2000000 INFO @ Sat, 11 Dec 2021 15:56:49: 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 15:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.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 15:56:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:56:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:56:57: 4000000 INFO @ Sat, 11 Dec 2021 15:57:05: 5000000 INFO @ Sat, 11 Dec 2021 15:57:06: 1000000 INFO @ Sat, 11 Dec 2021 15:57:12: 6000000 INFO @ Sat, 11 Dec 2021 15:57:17: 2000000 INFO @ Sat, 11 Dec 2021 15:57:20: 7000000 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 15:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.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 15:57:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:57:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:57:28: 3000000 INFO @ Sat, 11 Dec 2021 15:57:28: 8000000 INFO @ Sat, 11 Dec 2021 15:57:34: 1000000 INFO @ Sat, 11 Dec 2021 15:57:37: 9000000 INFO @ Sat, 11 Dec 2021 15:57:39: 4000000 INFO @ Sat, 11 Dec 2021 15:57:43: 2000000 INFO @ Sat, 11 Dec 2021 15:57:47: 10000000 INFO @ Sat, 11 Dec 2021 15:57:50: 5000000 INFO @ Sat, 11 Dec 2021 15:57:53: 3000000 INFO @ Sat, 11 Dec 2021 15:57:56: 11000000 INFO @ Sat, 11 Dec 2021 15:58:01: 6000000 INFO @ Sat, 11 Dec 2021 15:58:01: 4000000 INFO @ Sat, 11 Dec 2021 15:58:05: 12000000 INFO @ Sat, 11 Dec 2021 15:58:10: 5000000 INFO @ Sat, 11 Dec 2021 15:58:12: 7000000 INFO @ Sat, 11 Dec 2021 15:58:13: 13000000 INFO @ Sat, 11 Dec 2021 15:58:18: 6000000 INFO @ Sat, 11 Dec 2021 15:58:21: 14000000 INFO @ Sat, 11 Dec 2021 15:58:23: 8000000 INFO @ Sat, 11 Dec 2021 15:58:26: 7000000 INFO @ Sat, 11 Dec 2021 15:58:29: 15000000 INFO @ Sat, 11 Dec 2021 15:58:34: 9000000 INFO @ Sat, 11 Dec 2021 15:58:34: 8000000 INFO @ Sat, 11 Dec 2021 15:58:38: 16000000 INFO @ Sat, 11 Dec 2021 15:58:42: 9000000 INFO @ Sat, 11 Dec 2021 15:58:45: 10000000 INFO @ Sat, 11 Dec 2021 15:58:46: 17000000 INFO @ Sat, 11 Dec 2021 15:58:51: 10000000 INFO @ Sat, 11 Dec 2021 15:58:55: 18000000 INFO @ Sat, 11 Dec 2021 15:58:56: 11000000 INFO @ Sat, 11 Dec 2021 15:58:59: 11000000 INFO @ Sat, 11 Dec 2021 15:59:05: 19000000 INFO @ Sat, 11 Dec 2021 15:59:07: 12000000 INFO @ Sat, 11 Dec 2021 15:59:07: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 15:59:07: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 15:59:07: #1 total tags in treatment: 19290103 INFO @ Sat, 11 Dec 2021 15:59:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:59:07: #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 15:59:08: 12000000 INFO @ Sat, 11 Dec 2021 15:59:08: #1 tags after filtering in treatment: 19290103 INFO @ Sat, 11 Dec 2021 15:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:59:08: #1 finished! INFO @ Sat, 11 Dec 2021 15:59:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:59:10: #2 number of paired peaks: 319 WARNING @ Sat, 11 Dec 2021 15:59:10: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 11 Dec 2021 15:59:10: start model_add_line... INFO @ Sat, 11 Dec 2021 15:59:10: start X-correlation... INFO @ Sat, 11 Dec 2021 15:59:10: end of X-cor INFO @ Sat, 11 Dec 2021 15:59:10: #2 finished! INFO @ Sat, 11 Dec 2021 15:59:10: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 15:59:10: #2 alternative fragment length(s) may be 3,44,598 bps INFO @ Sat, 11 Dec 2021 15:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.05_model.r WARNING @ Sat, 11 Dec 2021 15:59:10: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:59:10: #2 You may need to consider one of the other alternative d(s): 3,44,598 WARNING @ Sat, 11 Dec 2021 15:59:10: #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 15:59:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:59:16: 13000000 INFO @ Sat, 11 Dec 2021 15:59:18: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:59:24: 14000000 INFO @ Sat, 11 Dec 2021 15:59:29: 14000000 INFO @ Sat, 11 Dec 2021 15:59:33: 15000000 INFO @ Sat, 11 Dec 2021 15:59:40: 15000000 INFO @ Sat, 11 Dec 2021 15:59:42: 16000000 INFO @ Sat, 11 Dec 2021 15:59:50: 17000000 INFO @ Sat, 11 Dec 2021 15:59:52: 16000000 INFO @ Sat, 11 Dec 2021 15:59:58: 18000000 INFO @ Sat, 11 Dec 2021 16:00:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:00:03: 17000000 INFO @ Sat, 11 Dec 2021 16:00:07: 19000000 INFO @ Sat, 11 Dec 2021 16:00:09: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 16:00:09: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 16:00:09: #1 total tags in treatment: 19290103 INFO @ Sat, 11 Dec 2021 16:00:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:00:09: #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 16:00:10: #1 tags after filtering in treatment: 19290103 INFO @ Sat, 11 Dec 2021 16:00:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:00:10: #1 finished! INFO @ Sat, 11 Dec 2021 16:00:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:00:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:00:12: #2 number of paired peaks: 319 WARNING @ Sat, 11 Dec 2021 16:00:12: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 11 Dec 2021 16:00:12: start model_add_line... INFO @ Sat, 11 Dec 2021 16:00:12: start X-correlation... INFO @ Sat, 11 Dec 2021 16:00:12: end of X-cor INFO @ Sat, 11 Dec 2021 16:00:12: #2 finished! INFO @ Sat, 11 Dec 2021 16:00:12: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 16:00:12: #2 alternative fragment length(s) may be 3,44,598 bps INFO @ Sat, 11 Dec 2021 16:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.20_model.r WARNING @ Sat, 11 Dec 2021 16:00:12: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:00:12: #2 You may need to consider one of the other alternative d(s): 3,44,598 WARNING @ Sat, 11 Dec 2021 16:00:12: #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 16:00:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:00:15: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.05_summits.bed INFO @ Sat, 11 Dec 2021 16:00:25: Done! INFO @ Sat, 11 Dec 2021 16:00:26: 19000000 pass1 - making usageList (521 chroms): 4 millis pass2 - checking and writing primary data (5543 records, 4 fields): 227 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:00:29: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 16:00:29: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 16:00:29: #1 total tags in treatment: 19290103 INFO @ Sat, 11 Dec 2021 16:00:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:00:29: #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 16:00:29: #1 tags after filtering in treatment: 19290103 INFO @ Sat, 11 Dec 2021 16:00:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:00:29: #1 finished! INFO @ Sat, 11 Dec 2021 16:00:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:00:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:00:31: #2 number of paired peaks: 319 WARNING @ Sat, 11 Dec 2021 16:00:31: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sat, 11 Dec 2021 16:00:31: start model_add_line... INFO @ Sat, 11 Dec 2021 16:00:31: start X-correlation... INFO @ Sat, 11 Dec 2021 16:00:31: end of X-cor INFO @ Sat, 11 Dec 2021 16:00:31: #2 finished! INFO @ Sat, 11 Dec 2021 16:00:31: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 16:00:31: #2 alternative fragment length(s) may be 3,44,598 bps INFO @ Sat, 11 Dec 2021 16:00:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.10_model.r WARNING @ Sat, 11 Dec 2021 16:00:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:00:31: #2 You may need to consider one of the other alternative d(s): 3,44,598 WARNING @ Sat, 11 Dec 2021 16:00:31: #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 16:00:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:00:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:01:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:01:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.20_summits.bed INFO @ Sat, 11 Dec 2021 16:01:27: Done! pass1 - making usageList (231 chroms): 2 millis pass2 - checking and writing primary data (518 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089753/SRX10089753.10_summits.bed INFO @ Sat, 11 Dec 2021 16:01:44: Done! pass1 - making usageList (449 chroms): 3 millis pass2 - checking and writing primary data (2430 records, 4 fields): 24 millis CompletedMACS2peakCalling