Job ID = 16438528 SRX = SRX10031706 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: 00:00:01 Multiseed full-index search: 00:12:22 38372925 reads; of these: 38372925 (100.00%) were unpaired; of these: 2430925 (6.34%) aligned 0 times 27756287 (72.33%) aligned exactly 1 time 8185713 (21.33%) aligned >1 times 93.66% overall alignment rate Time searching: 00:12:23 Overall time: 00:12:23 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 16 files... [bam_rmdupse_core] 7241986 / 35942000 = 0.2015 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:18:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.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 @ Tue, 02 Aug 2022 14:18:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:04: 1000000 INFO @ Tue, 02 Aug 2022 14:19:10: 2000000 INFO @ Tue, 02 Aug 2022 14:19:16: 3000000 INFO @ Tue, 02 Aug 2022 14:19:22: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:19:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.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 @ Tue, 02 Aug 2022 14:19:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:28: 5000000 INFO @ Tue, 02 Aug 2022 14:19:34: 1000000 INFO @ Tue, 02 Aug 2022 14:19:34: 6000000 INFO @ Tue, 02 Aug 2022 14:19:41: 2000000 INFO @ Tue, 02 Aug 2022 14:19:41: 7000000 INFO @ Tue, 02 Aug 2022 14:19:47: 8000000 INFO @ Tue, 02 Aug 2022 14:19:47: 3000000 INFO @ Tue, 02 Aug 2022 14:19:53: 4000000 INFO @ Tue, 02 Aug 2022 14:19:53: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.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 @ Tue, 02 Aug 2022 14:19:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:59: 5000000 INFO @ Tue, 02 Aug 2022 14:19:59: 10000000 INFO @ Tue, 02 Aug 2022 14:20:03: 1000000 INFO @ Tue, 02 Aug 2022 14:20:05: 6000000 INFO @ Tue, 02 Aug 2022 14:20:06: 11000000 INFO @ Tue, 02 Aug 2022 14:20:09: 2000000 INFO @ Tue, 02 Aug 2022 14:20:12: 7000000 INFO @ Tue, 02 Aug 2022 14:20:12: 12000000 INFO @ Tue, 02 Aug 2022 14:20:14: 3000000 INFO @ Tue, 02 Aug 2022 14:20:18: 8000000 INFO @ Tue, 02 Aug 2022 14:20:18: 13000000 INFO @ Tue, 02 Aug 2022 14:20:19: 4000000 INFO @ Tue, 02 Aug 2022 14:20:24: 9000000 INFO @ Tue, 02 Aug 2022 14:20:25: 14000000 INFO @ Tue, 02 Aug 2022 14:20:25: 5000000 INFO @ Tue, 02 Aug 2022 14:20:31: 10000000 INFO @ Tue, 02 Aug 2022 14:20:31: 6000000 INFO @ Tue, 02 Aug 2022 14:20:31: 15000000 INFO @ Tue, 02 Aug 2022 14:20:36: 7000000 INFO @ Tue, 02 Aug 2022 14:20:37: 11000000 INFO @ Tue, 02 Aug 2022 14:20:37: 16000000 INFO @ Tue, 02 Aug 2022 14:20:42: 8000000 INFO @ Tue, 02 Aug 2022 14:20:43: 12000000 INFO @ Tue, 02 Aug 2022 14:20:44: 17000000 INFO @ Tue, 02 Aug 2022 14:20:47: 9000000 INFO @ Tue, 02 Aug 2022 14:20:49: 13000000 INFO @ Tue, 02 Aug 2022 14:20:50: 18000000 INFO @ Tue, 02 Aug 2022 14:20:53: 10000000 INFO @ Tue, 02 Aug 2022 14:20:55: 14000000 INFO @ Tue, 02 Aug 2022 14:20:56: 19000000 INFO @ Tue, 02 Aug 2022 14:20:58: 11000000 INFO @ Tue, 02 Aug 2022 14:21:01: 15000000 INFO @ Tue, 02 Aug 2022 14:21:02: 20000000 INFO @ Tue, 02 Aug 2022 14:21:04: 12000000 INFO @ Tue, 02 Aug 2022 14:21:07: 16000000 INFO @ Tue, 02 Aug 2022 14:21:09: 21000000 INFO @ Tue, 02 Aug 2022 14:21:09: 13000000 INFO @ Tue, 02 Aug 2022 14:21:13: 17000000 INFO @ Tue, 02 Aug 2022 14:21:14: 14000000 INFO @ Tue, 02 Aug 2022 14:21:15: 22000000 INFO @ Tue, 02 Aug 2022 14:21:19: 18000000 INFO @ Tue, 02 Aug 2022 14:21:20: 15000000 INFO @ Tue, 02 Aug 2022 14:21:21: 23000000 INFO @ Tue, 02 Aug 2022 14:21:25: 19000000 INFO @ Tue, 02 Aug 2022 14:21:25: 16000000 INFO @ Tue, 02 Aug 2022 14:21:27: 24000000 INFO @ Tue, 02 Aug 2022 14:21:31: 17000000 INFO @ Tue, 02 Aug 2022 14:21:31: 20000000 INFO @ Tue, 02 Aug 2022 14:21:34: 25000000 INFO @ Tue, 02 Aug 2022 14:21:36: 18000000 INFO @ Tue, 02 Aug 2022 14:21:36: 21000000 INFO @ Tue, 02 Aug 2022 14:21:40: 26000000 INFO @ Tue, 02 Aug 2022 14:21:41: 19000000 INFO @ Tue, 02 Aug 2022 14:21:42: 22000000 INFO @ Tue, 02 Aug 2022 14:21:46: 27000000 INFO @ Tue, 02 Aug 2022 14:21:46: 20000000 INFO @ Tue, 02 Aug 2022 14:21:48: 23000000 INFO @ Tue, 02 Aug 2022 14:21:52: 21000000 INFO @ Tue, 02 Aug 2022 14:21:52: 28000000 INFO @ Tue, 02 Aug 2022 14:21:54: 24000000 INFO @ Tue, 02 Aug 2022 14:21:57: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:21:57: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:21:57: #1 total tags in treatment: 28700014 INFO @ Tue, 02 Aug 2022 14:21:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:21:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:21:57: 22000000 INFO @ Tue, 02 Aug 2022 14:21:58: #1 tags after filtering in treatment: 28699990 INFO @ Tue, 02 Aug 2022 14:21:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:21:58: #1 finished! INFO @ Tue, 02 Aug 2022 14:21:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:21:59: 25000000 INFO @ Tue, 02 Aug 2022 14:21:59: #2 number of paired peaks: 281 WARNING @ Tue, 02 Aug 2022 14:21:59: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 02 Aug 2022 14:21:59: start model_add_line... INFO @ Tue, 02 Aug 2022 14:22:00: start X-correlation... INFO @ Tue, 02 Aug 2022 14:22:00: end of X-cor INFO @ Tue, 02 Aug 2022 14:22:00: #2 finished! INFO @ Tue, 02 Aug 2022 14:22:00: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 14:22:00: #2 alternative fragment length(s) may be 1,68 bps INFO @ Tue, 02 Aug 2022 14:22:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.05_model.r WARNING @ Tue, 02 Aug 2022 14:22:00: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:22:00: #2 You may need to consider one of the other alternative d(s): 1,68 WARNING @ Tue, 02 Aug 2022 14:22:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:22:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:22:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:22:03: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:22:05: 26000000 INFO @ Tue, 02 Aug 2022 14:22:09: 24000000 INFO @ Tue, 02 Aug 2022 14:22:10: 27000000 INFO @ Tue, 02 Aug 2022 14:22:15: 25000000 INFO @ Tue, 02 Aug 2022 14:22:16: 28000000 INFO @ Tue, 02 Aug 2022 14:22:21: 26000000 INFO @ Tue, 02 Aug 2022 14:22:21: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:22:21: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:22:21: #1 total tags in treatment: 28700014 INFO @ Tue, 02 Aug 2022 14:22:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:22:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:22:21: #1 tags after filtering in treatment: 28699990 INFO @ Tue, 02 Aug 2022 14:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:22:21: #1 finished! INFO @ Tue, 02 Aug 2022 14:22:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:22:23: #2 number of paired peaks: 281 WARNING @ Tue, 02 Aug 2022 14:22:23: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 02 Aug 2022 14:22:23: start model_add_line... INFO @ Tue, 02 Aug 2022 14:22:23: start X-correlation... INFO @ Tue, 02 Aug 2022 14:22:23: end of X-cor INFO @ Tue, 02 Aug 2022 14:22:23: #2 finished! INFO @ Tue, 02 Aug 2022 14:22:23: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 14:22:23: #2 alternative fragment length(s) may be 1,68 bps INFO @ Tue, 02 Aug 2022 14:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.10_model.r WARNING @ Tue, 02 Aug 2022 14:22:23: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:22:23: #2 You may need to consider one of the other alternative d(s): 1,68 WARNING @ Tue, 02 Aug 2022 14:22:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:22:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:22:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:22:26: 27000000 INFO @ Tue, 02 Aug 2022 14:22:32: 28000000 INFO @ Tue, 02 Aug 2022 14:22:36: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:22:36: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:22:36: #1 total tags in treatment: 28700014 INFO @ Tue, 02 Aug 2022 14:22:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:22:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:22:37: #1 tags after filtering in treatment: 28699990 INFO @ Tue, 02 Aug 2022 14:22:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:22:37: #1 finished! INFO @ Tue, 02 Aug 2022 14:22:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:22:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:22:39: #2 number of paired peaks: 281 WARNING @ Tue, 02 Aug 2022 14:22:39: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 02 Aug 2022 14:22:39: start model_add_line... INFO @ Tue, 02 Aug 2022 14:22:39: start X-correlation... INFO @ Tue, 02 Aug 2022 14:22:39: end of X-cor INFO @ Tue, 02 Aug 2022 14:22:39: #2 finished! INFO @ Tue, 02 Aug 2022 14:22:39: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 14:22:39: #2 alternative fragment length(s) may be 1,68 bps INFO @ Tue, 02 Aug 2022 14:22:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.20_model.r WARNING @ Tue, 02 Aug 2022 14:22:39: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:22:39: #2 You may need to consider one of the other alternative d(s): 1,68 WARNING @ Tue, 02 Aug 2022 14:22:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:22:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:22:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:22:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:23:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:23:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:23:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.05_summits.bed INFO @ Tue, 02 Aug 2022 14:23:09: Done! pass1 - making usageList (558 chroms): 1 millis pass2 - checking and writing primary data (3182 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:23:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:23:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.10_summits.bed INFO @ Tue, 02 Aug 2022 14:23:33: Done! pass1 - making usageList (458 chroms): 1 millis pass2 - checking and writing primary data (1672 records, 4 fields): 433 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:23:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031706/SRX10031706.20_summits.bed INFO @ Tue, 02 Aug 2022 14:23:49: Done! pass1 - making usageList (277 chroms): 1 millis pass2 - checking and writing primary data (677 records, 4 fields): 26 millis CompletedMACS2peakCalling