Job ID = 14171672 SRX = SRX9986111 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: 00:06:30 27353650 reads; of these: 27353650 (100.00%) were unpaired; of these: 2497446 (9.13%) aligned 0 times 18215064 (66.59%) aligned exactly 1 time 6641140 (24.28%) aligned >1 times 90.87% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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_sort_core] merging from 12 files... [bam_rmdupse_core] 6242775 / 24856204 = 0.2512 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 12:33:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.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 12:33:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:33:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:33:35: 1000000 INFO @ Sat, 11 Dec 2021 12:33:39: 2000000 INFO @ Sat, 11 Dec 2021 12:33:44: 3000000 INFO @ Sat, 11 Dec 2021 12:33:48: 4000000 INFO @ Sat, 11 Dec 2021 12:33:53: 5000000 INFO @ Sat, 11 Dec 2021 12:33:57: 6000000 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 12:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.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 12:34:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:34:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:34:02: 7000000 INFO @ Sat, 11 Dec 2021 12:34:05: 1000000 INFO @ Sat, 11 Dec 2021 12:34:07: 8000000 INFO @ Sat, 11 Dec 2021 12:34:09: 2000000 INFO @ Sat, 11 Dec 2021 12:34:11: 9000000 INFO @ Sat, 11 Dec 2021 12:34:14: 3000000 INFO @ Sat, 11 Dec 2021 12:34:16: 10000000 INFO @ Sat, 11 Dec 2021 12:34:19: 4000000 INFO @ Sat, 11 Dec 2021 12:34:21: 11000000 INFO @ Sat, 11 Dec 2021 12:34:23: 5000000 INFO @ Sat, 11 Dec 2021 12:34:25: 12000000 INFO @ Sat, 11 Dec 2021 12:34:28: 6000000 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 12:34:30: 13000000 INFO @ Sat, 11 Dec 2021 12:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.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 12:34:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:34:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:34:33: 7000000 INFO @ Sat, 11 Dec 2021 12:34:35: 14000000 INFO @ Sat, 11 Dec 2021 12:34:35: 1000000 INFO @ Sat, 11 Dec 2021 12:34:38: 8000000 INFO @ Sat, 11 Dec 2021 12:34:40: 15000000 INFO @ Sat, 11 Dec 2021 12:34:40: 2000000 INFO @ Sat, 11 Dec 2021 12:34:42: 9000000 INFO @ Sat, 11 Dec 2021 12:34:44: 16000000 INFO @ Sat, 11 Dec 2021 12:34:44: 3000000 INFO @ Sat, 11 Dec 2021 12:34:47: 10000000 INFO @ Sat, 11 Dec 2021 12:34:49: 17000000 INFO @ Sat, 11 Dec 2021 12:34:49: 4000000 INFO @ Sat, 11 Dec 2021 12:34:52: 11000000 INFO @ Sat, 11 Dec 2021 12:34:54: 18000000 INFO @ Sat, 11 Dec 2021 12:34:54: 5000000 INFO @ Sat, 11 Dec 2021 12:34:57: 12000000 INFO @ Sat, 11 Dec 2021 12:34:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:34:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:34:57: #1 total tags in treatment: 18613429 INFO @ Sat, 11 Dec 2021 12:34:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:34:57: #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 12:34:57: #1 tags after filtering in treatment: 18613383 INFO @ Sat, 11 Dec 2021 12:34:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:34:57: #1 finished! INFO @ Sat, 11 Dec 2021 12:34:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:34:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:34:59: #2 number of paired peaks: 109 WARNING @ Sat, 11 Dec 2021 12:34:59: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 11 Dec 2021 12:34:59: start model_add_line... INFO @ Sat, 11 Dec 2021 12:34:59: 6000000 INFO @ Sat, 11 Dec 2021 12:34:59: start X-correlation... INFO @ Sat, 11 Dec 2021 12:34:59: end of X-cor INFO @ Sat, 11 Dec 2021 12:34:59: #2 finished! INFO @ Sat, 11 Dec 2021 12:34:59: #2 predicted fragment length is 11 bps INFO @ Sat, 11 Dec 2021 12:34:59: #2 alternative fragment length(s) may be 11,32,48,422,515,528,563 bps INFO @ Sat, 11 Dec 2021 12:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.05_model.r WARNING @ Sat, 11 Dec 2021 12:34:59: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:34:59: #2 You may need to consider one of the other alternative d(s): 11,32,48,422,515,528,563 WARNING @ Sat, 11 Dec 2021 12:34:59: #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 12:34:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:35:01: 13000000 INFO @ Sat, 11 Dec 2021 12:35:03: 7000000 INFO @ Sat, 11 Dec 2021 12:35:06: 14000000 INFO @ Sat, 11 Dec 2021 12:35:08: 8000000 INFO @ Sat, 11 Dec 2021 12:35:11: 15000000 INFO @ Sat, 11 Dec 2021 12:35:13: 9000000 INFO @ Sat, 11 Dec 2021 12:35:16: 16000000 INFO @ Sat, 11 Dec 2021 12:35:17: 10000000 INFO @ Sat, 11 Dec 2021 12:35:21: 17000000 INFO @ Sat, 11 Dec 2021 12:35:22: 11000000 INFO @ Sat, 11 Dec 2021 12:35:25: 18000000 INFO @ Sat, 11 Dec 2021 12:35:27: 12000000 INFO @ Sat, 11 Dec 2021 12:35:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:35:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:35:29: #1 total tags in treatment: 18613429 INFO @ Sat, 11 Dec 2021 12:35:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:35:29: #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 12:35:29: #1 tags after filtering in treatment: 18613383 INFO @ Sat, 11 Dec 2021 12:35:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:35:29: #1 finished! INFO @ Sat, 11 Dec 2021 12:35:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:35:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:35:30: #2 number of paired peaks: 109 WARNING @ Sat, 11 Dec 2021 12:35:30: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 11 Dec 2021 12:35:30: start model_add_line... INFO @ Sat, 11 Dec 2021 12:35:30: start X-correlation... INFO @ Sat, 11 Dec 2021 12:35:30: end of X-cor INFO @ Sat, 11 Dec 2021 12:35:30: #2 finished! INFO @ Sat, 11 Dec 2021 12:35:30: #2 predicted fragment length is 11 bps INFO @ Sat, 11 Dec 2021 12:35:30: #2 alternative fragment length(s) may be 11,32,48,422,515,528,563 bps INFO @ Sat, 11 Dec 2021 12:35:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.10_model.r WARNING @ Sat, 11 Dec 2021 12:35:30: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:35:30: #2 You may need to consider one of the other alternative d(s): 11,32,48,422,515,528,563 WARNING @ Sat, 11 Dec 2021 12:35:30: #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 12:35:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:35:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:35:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:35:32: 13000000 INFO @ Sat, 11 Dec 2021 12:35:36: 14000000 INFO @ Sat, 11 Dec 2021 12:35:41: 15000000 INFO @ Sat, 11 Dec 2021 12:35:46: 16000000 INFO @ Sat, 11 Dec 2021 12:35:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.05_summits.bed INFO @ Sat, 11 Dec 2021 12:35:46: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:35:50: 17000000 INFO @ Sat, 11 Dec 2021 12:35:55: 18000000 INFO @ Sat, 11 Dec 2021 12:35:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:35:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:35:58: #1 total tags in treatment: 18613429 INFO @ Sat, 11 Dec 2021 12:35:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:35:58: #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 12:35:59: #1 tags after filtering in treatment: 18613383 INFO @ Sat, 11 Dec 2021 12:35:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:35:59: #1 finished! INFO @ Sat, 11 Dec 2021 12:35:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:35:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:36:00: #2 number of paired peaks: 109 WARNING @ Sat, 11 Dec 2021 12:36:00: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 11 Dec 2021 12:36:00: start model_add_line... INFO @ Sat, 11 Dec 2021 12:36:00: start X-correlation... INFO @ Sat, 11 Dec 2021 12:36:00: end of X-cor INFO @ Sat, 11 Dec 2021 12:36:00: #2 finished! INFO @ Sat, 11 Dec 2021 12:36:00: #2 predicted fragment length is 11 bps INFO @ Sat, 11 Dec 2021 12:36:00: #2 alternative fragment length(s) may be 11,32,48,422,515,528,563 bps INFO @ Sat, 11 Dec 2021 12:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.20_model.r WARNING @ Sat, 11 Dec 2021 12:36:00: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:36:00: #2 You may need to consider one of the other alternative d(s): 11,32,48,422,515,528,563 WARNING @ Sat, 11 Dec 2021 12:36:00: #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 12:36:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:36:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:36:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.10_summits.bed INFO @ Sat, 11 Dec 2021 12:36:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:36:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986111/SRX9986111.20_summits.bed INFO @ Sat, 11 Dec 2021 12:36:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling