Job ID = 14172420 SRX = SRX3292999 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: 00:17:47 23173312 reads; of these: 23173312 (100.00%) were unpaired; of these: 648228 (2.80%) aligned 0 times 18819716 (81.21%) aligned exactly 1 time 3705368 (15.99%) aligned >1 times 97.20% overall alignment rate Time searching: 00:17:48 Overall time: 00:17:48 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] 2213512 / 22525084 = 0.0983 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 15:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.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 15:53:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:53:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:53:40: 1000000 INFO @ Sat, 11 Dec 2021 15:53:53: 2000000 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 15:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.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 15:53:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:53:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:54:05: 3000000 INFO @ Sat, 11 Dec 2021 15:54:13: 1000000 INFO @ Sat, 11 Dec 2021 15:54:17: 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 15:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.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 15:54:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:54:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:54:28: 2000000 INFO @ Sat, 11 Dec 2021 15:54:29: 5000000 INFO @ Sat, 11 Dec 2021 15:54:42: 6000000 INFO @ Sat, 11 Dec 2021 15:54:43: 1000000 INFO @ Sat, 11 Dec 2021 15:54:43: 3000000 INFO @ Sat, 11 Dec 2021 15:54:55: 7000000 INFO @ Sat, 11 Dec 2021 15:54:58: 2000000 INFO @ Sat, 11 Dec 2021 15:54:59: 4000000 INFO @ Sat, 11 Dec 2021 15:55:07: 8000000 INFO @ Sat, 11 Dec 2021 15:55:11: 3000000 INFO @ Sat, 11 Dec 2021 15:55:12: 5000000 INFO @ Sat, 11 Dec 2021 15:55:19: 9000000 INFO @ Sat, 11 Dec 2021 15:55:25: 4000000 INFO @ Sat, 11 Dec 2021 15:55:26: 6000000 INFO @ Sat, 11 Dec 2021 15:55:34: 10000000 INFO @ Sat, 11 Dec 2021 15:55:39: 5000000 INFO @ Sat, 11 Dec 2021 15:55:40: 7000000 INFO @ Sat, 11 Dec 2021 15:55:47: 11000000 INFO @ Sat, 11 Dec 2021 15:55:52: 6000000 INFO @ Sat, 11 Dec 2021 15:55:54: 8000000 INFO @ Sat, 11 Dec 2021 15:56:00: 12000000 INFO @ Sat, 11 Dec 2021 15:56:06: 7000000 INFO @ Sat, 11 Dec 2021 15:56:08: 9000000 INFO @ Sat, 11 Dec 2021 15:56:12: 13000000 INFO @ Sat, 11 Dec 2021 15:56:20: 8000000 INFO @ Sat, 11 Dec 2021 15:56:22: 10000000 INFO @ Sat, 11 Dec 2021 15:56:24: 14000000 INFO @ Sat, 11 Dec 2021 15:56:33: 9000000 INFO @ Sat, 11 Dec 2021 15:56:36: 11000000 INFO @ Sat, 11 Dec 2021 15:56:37: 15000000 INFO @ Sat, 11 Dec 2021 15:56:46: 10000000 INFO @ Sat, 11 Dec 2021 15:56:50: 16000000 INFO @ Sat, 11 Dec 2021 15:56:50: 12000000 INFO @ Sat, 11 Dec 2021 15:57:00: 11000000 INFO @ Sat, 11 Dec 2021 15:57:03: 17000000 INFO @ Sat, 11 Dec 2021 15:57:03: 13000000 INFO @ Sat, 11 Dec 2021 15:57:15: 12000000 INFO @ Sat, 11 Dec 2021 15:57:16: 18000000 INFO @ Sat, 11 Dec 2021 15:57:18: 14000000 INFO @ Sat, 11 Dec 2021 15:57:28: 13000000 INFO @ Sat, 11 Dec 2021 15:57:28: 19000000 INFO @ Sat, 11 Dec 2021 15:57:32: 15000000 INFO @ Sat, 11 Dec 2021 15:57:41: 20000000 INFO @ Sat, 11 Dec 2021 15:57:42: 14000000 INFO @ Sat, 11 Dec 2021 15:57:45: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:57:45: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:57:45: #1 total tags in treatment: 20311572 INFO @ Sat, 11 Dec 2021 15:57:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:57:45: #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 15:57:45: 16000000 INFO @ Sat, 11 Dec 2021 15:57:46: #1 tags after filtering in treatment: 20311403 INFO @ Sat, 11 Dec 2021 15:57:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:57:46: #1 finished! INFO @ Sat, 11 Dec 2021 15:57:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:57:48: #2 number of paired peaks: 310 WARNING @ Sat, 11 Dec 2021 15:57:48: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 11 Dec 2021 15:57:48: start model_add_line... INFO @ Sat, 11 Dec 2021 15:57:48: start X-correlation... INFO @ Sat, 11 Dec 2021 15:57:48: end of X-cor INFO @ Sat, 11 Dec 2021 15:57:48: #2 finished! INFO @ Sat, 11 Dec 2021 15:57:48: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 15:57:48: #2 alternative fragment length(s) may be 2,84,105 bps INFO @ Sat, 11 Dec 2021 15:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.05_model.r WARNING @ Sat, 11 Dec 2021 15:57:48: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:57:48: #2 You may need to consider one of the other alternative d(s): 2,84,105 WARNING @ Sat, 11 Dec 2021 15:57:48: #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 15:57:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:57:56: 15000000 INFO @ Sat, 11 Dec 2021 15:58:00: 17000000 INFO @ Sat, 11 Dec 2021 15:58:09: 16000000 INFO @ Sat, 11 Dec 2021 15:58:14: 18000000 INFO @ Sat, 11 Dec 2021 15:58:24: 17000000 INFO @ Sat, 11 Dec 2021 15:58:29: 19000000 INFO @ Sat, 11 Dec 2021 15:58:39: 18000000 INFO @ Sat, 11 Dec 2021 15:58:43: 20000000 INFO @ Sat, 11 Dec 2021 15:58:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:58:48: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:58:48: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:58:48: #1 total tags in treatment: 20311572 INFO @ Sat, 11 Dec 2021 15:58:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:58:48: #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 15:58:49: #1 tags after filtering in treatment: 20311403 INFO @ Sat, 11 Dec 2021 15:58:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:58:49: #1 finished! INFO @ Sat, 11 Dec 2021 15:58:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:58:51: #2 number of paired peaks: 310 WARNING @ Sat, 11 Dec 2021 15:58:51: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 11 Dec 2021 15:58:51: start model_add_line... INFO @ Sat, 11 Dec 2021 15:58:51: start X-correlation... INFO @ Sat, 11 Dec 2021 15:58:51: end of X-cor INFO @ Sat, 11 Dec 2021 15:58:51: #2 finished! INFO @ Sat, 11 Dec 2021 15:58:51: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 15:58:51: #2 alternative fragment length(s) may be 2,84,105 bps INFO @ Sat, 11 Dec 2021 15:58:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.10_model.r WARNING @ Sat, 11 Dec 2021 15:58:51: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:58:51: #2 You may need to consider one of the other alternative d(s): 2,84,105 WARNING @ Sat, 11 Dec 2021 15:58:51: #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 15:58:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:58:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:58:53: 19000000 INFO @ Sat, 11 Dec 2021 15:59:05: 20000000 INFO @ Sat, 11 Dec 2021 15:59:09: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:59:09: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:59:09: #1 total tags in treatment: 20311572 INFO @ Sat, 11 Dec 2021 15:59:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:59:09: #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 15:59:10: #1 tags after filtering in treatment: 20311403 INFO @ Sat, 11 Dec 2021 15:59:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:59:10: #1 finished! INFO @ Sat, 11 Dec 2021 15:59:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:59:12: #2 number of paired peaks: 310 WARNING @ Sat, 11 Dec 2021 15:59:12: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 11 Dec 2021 15:59:12: start model_add_line... INFO @ Sat, 11 Dec 2021 15:59:12: start X-correlation... INFO @ Sat, 11 Dec 2021 15:59:12: end of X-cor INFO @ Sat, 11 Dec 2021 15:59:12: #2 finished! INFO @ Sat, 11 Dec 2021 15:59:12: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 15:59:12: #2 alternative fragment length(s) may be 2,84,105 bps INFO @ Sat, 11 Dec 2021 15:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.20_model.r WARNING @ Sat, 11 Dec 2021 15:59:12: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:59:12: #2 You may need to consider one of the other alternative d(s): 2,84,105 WARNING @ Sat, 11 Dec 2021 15:59:12: #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 15:59:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:59:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:59:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:59:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.05_summits.bed INFO @ Sat, 11 Dec 2021 15:59:14: Done! pass1 - making usageList (402 chroms): 1 millis pass2 - checking and writing primary data (1143 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:59:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:00:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.10_summits.bed INFO @ Sat, 11 Dec 2021 16:00:18: Done! pass1 - making usageList (265 chroms): 2 millis pass2 - checking and writing primary data (631 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:00:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:00:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:00:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3292999/SRX3292999.20_summits.bed INFO @ Sat, 11 Dec 2021 16:00:38: Done! pass1 - making usageList (152 chroms): 2 millis pass2 - checking and writing primary data (334 records, 4 fields): 12 millis CompletedMACS2peakCalling