Job ID = 14170371 SRX = SRX9720906 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26075110 spots for SRR13291896/SRR13291896.sra Written 26075110 spots for SRR13291896/SRR13291896.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170775 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:14 26075110 reads; of these: 26075110 (100.00%) were unpaired; of these: 948137 (3.64%) aligned 0 times 16804594 (64.45%) aligned exactly 1 time 8322379 (31.92%) aligned >1 times 96.36% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3263500 / 25126973 = 0.1299 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 06:39:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.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 06:39:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:54: 1000000 INFO @ Sat, 11 Dec 2021 06:40:00: 2000000 INFO @ Sat, 11 Dec 2021 06:40:07: 3000000 INFO @ Sat, 11 Dec 2021 06:40:13: 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 06:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.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 06:40:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:20: 5000000 INFO @ Sat, 11 Dec 2021 06:40:22: 1000000 INFO @ Sat, 11 Dec 2021 06:40:26: 6000000 INFO @ Sat, 11 Dec 2021 06:40:28: 2000000 INFO @ Sat, 11 Dec 2021 06:40:33: 3000000 INFO @ Sat, 11 Dec 2021 06:40:33: 7000000 INFO @ Sat, 11 Dec 2021 06:40:38: 4000000 INFO @ Sat, 11 Dec 2021 06:40:40: 8000000 INFO @ Sat, 11 Dec 2021 06:40:44: 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 06:40:46: 9000000 INFO @ Sat, 11 Dec 2021 06:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.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 06:40:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:49: 6000000 INFO @ Sat, 11 Dec 2021 06:40:53: 1000000 INFO @ Sat, 11 Dec 2021 06:40:53: 10000000 INFO @ Sat, 11 Dec 2021 06:40:55: 7000000 INFO @ Sat, 11 Dec 2021 06:40:58: 2000000 INFO @ Sat, 11 Dec 2021 06:40:59: 11000000 INFO @ Sat, 11 Dec 2021 06:41:00: 8000000 INFO @ Sat, 11 Dec 2021 06:41:03: 3000000 INFO @ Sat, 11 Dec 2021 06:41:06: 9000000 INFO @ Sat, 11 Dec 2021 06:41:06: 12000000 INFO @ Sat, 11 Dec 2021 06:41:09: 4000000 INFO @ Sat, 11 Dec 2021 06:41:11: 10000000 INFO @ Sat, 11 Dec 2021 06:41:13: 13000000 INFO @ Sat, 11 Dec 2021 06:41:14: 5000000 INFO @ Sat, 11 Dec 2021 06:41:16: 11000000 INFO @ Sat, 11 Dec 2021 06:41:19: 14000000 INFO @ Sat, 11 Dec 2021 06:41:20: 6000000 INFO @ Sat, 11 Dec 2021 06:41:22: 12000000 INFO @ Sat, 11 Dec 2021 06:41:25: 7000000 INFO @ Sat, 11 Dec 2021 06:41:26: 15000000 INFO @ Sat, 11 Dec 2021 06:41:27: 13000000 INFO @ Sat, 11 Dec 2021 06:41:30: 8000000 INFO @ Sat, 11 Dec 2021 06:41:33: 14000000 INFO @ Sat, 11 Dec 2021 06:41:33: 16000000 INFO @ Sat, 11 Dec 2021 06:41:36: 9000000 INFO @ Sat, 11 Dec 2021 06:41:38: 15000000 INFO @ Sat, 11 Dec 2021 06:41:39: 17000000 INFO @ Sat, 11 Dec 2021 06:41:41: 10000000 INFO @ Sat, 11 Dec 2021 06:41:44: 16000000 INFO @ Sat, 11 Dec 2021 06:41:46: 18000000 INFO @ Sat, 11 Dec 2021 06:41:47: 11000000 INFO @ Sat, 11 Dec 2021 06:41:49: 17000000 INFO @ Sat, 11 Dec 2021 06:41:52: 12000000 INFO @ Sat, 11 Dec 2021 06:41:52: 19000000 INFO @ Sat, 11 Dec 2021 06:41:54: 18000000 INFO @ Sat, 11 Dec 2021 06:41:57: 13000000 INFO @ Sat, 11 Dec 2021 06:41:59: 20000000 INFO @ Sat, 11 Dec 2021 06:42:00: 19000000 INFO @ Sat, 11 Dec 2021 06:42:03: 14000000 INFO @ Sat, 11 Dec 2021 06:42:05: 21000000 INFO @ Sat, 11 Dec 2021 06:42:05: 20000000 INFO @ Sat, 11 Dec 2021 06:42:08: 15000000 INFO @ Sat, 11 Dec 2021 06:42:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:11: #1 total tags in treatment: 21863473 INFO @ Sat, 11 Dec 2021 06:42:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:11: #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 06:42:11: 21000000 INFO @ Sat, 11 Dec 2021 06:42:11: #1 tags after filtering in treatment: 21863473 INFO @ Sat, 11 Dec 2021 06:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:11: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:13: #2 number of paired peaks: 324 WARNING @ Sat, 11 Dec 2021 06:42:13: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:13: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:13: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:13: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:13: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:13: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:42:13: #2 alternative fragment length(s) may be 2,50,543,551 bps INFO @ Sat, 11 Dec 2021 06:42:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.05_model.r WARNING @ Sat, 11 Dec 2021 06:42:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:42:13: #2 You may need to consider one of the other alternative d(s): 2,50,543,551 WARNING @ Sat, 11 Dec 2021 06:42:13: #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 06:42:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:14: 16000000 INFO @ Sat, 11 Dec 2021 06:42:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:15: #1 total tags in treatment: 21863473 INFO @ Sat, 11 Dec 2021 06:42:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:15: #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 06:42:16: #1 tags after filtering in treatment: 21863473 INFO @ Sat, 11 Dec 2021 06:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:16: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:17: #2 number of paired peaks: 324 WARNING @ Sat, 11 Dec 2021 06:42:17: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:17: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:17: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:17: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:17: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:17: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:42:17: #2 alternative fragment length(s) may be 2,50,543,551 bps INFO @ Sat, 11 Dec 2021 06:42:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.10_model.r WARNING @ Sat, 11 Dec 2021 06:42:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:42:17: #2 You may need to consider one of the other alternative d(s): 2,50,543,551 WARNING @ Sat, 11 Dec 2021 06:42:17: #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 06:42:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:19: 17000000 INFO @ Sat, 11 Dec 2021 06:42:24: 18000000 INFO @ Sat, 11 Dec 2021 06:42:29: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:42:34: 20000000 INFO @ Sat, 11 Dec 2021 06:42:39: 21000000 INFO @ Sat, 11 Dec 2021 06:42:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:44: #1 total tags in treatment: 21863473 INFO @ Sat, 11 Dec 2021 06:42:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:44: #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 06:42:44: #1 tags after filtering in treatment: 21863473 INFO @ Sat, 11 Dec 2021 06:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:44: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:46: #2 number of paired peaks: 324 WARNING @ Sat, 11 Dec 2021 06:42:46: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:46: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:46: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:46: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:46: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:46: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:42:46: #2 alternative fragment length(s) may be 2,50,543,551 bps INFO @ Sat, 11 Dec 2021 06:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.20_model.r WARNING @ Sat, 11 Dec 2021 06:42:46: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:42:46: #2 You may need to consider one of the other alternative d(s): 2,50,543,551 WARNING @ Sat, 11 Dec 2021 06:42:46: #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 06:42:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:43:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.10_summits.bed INFO @ Sat, 11 Dec 2021 06:43:21: Done! INFO @ Sat, 11 Dec 2021 06:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.05_summits.bed INFO @ Sat, 11 Dec 2021 06:43:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2118 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3266 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:43:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:43:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720906/SRX9720906.20_summits.bed INFO @ Sat, 11 Dec 2021 06:43:49: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (707 records, 4 fields): 2 millis CompletedMACS2peakCalling