Job ID = 16438427 SRX = SRX14148458 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: 00:31:03 57714836 reads; of these: 57714836 (100.00%) were unpaired; of these: 3779721 (6.55%) aligned 0 times 34625214 (59.99%) aligned exactly 1 time 19309901 (33.46%) aligned >1 times 93.45% overall alignment rate Time searching: 00:31:04 Overall time: 00:31:04 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 24 files... [bam_rmdupse_core] 15497979 / 53935115 = 0.2873 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 14:42:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.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 14:42:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:42:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:42:36: 1000000 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 14:42:50: 2000000 INFO @ Tue, 02 Aug 2022 14:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.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 14:42:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:42:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:43:03: 3000000 INFO @ Tue, 02 Aug 2022 14:43:05: 1000000 INFO @ Tue, 02 Aug 2022 14:43:15: 4000000 INFO @ Tue, 02 Aug 2022 14:43:17: 2000000 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 14:43:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.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 14:43:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:43:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:43:29: 5000000 INFO @ Tue, 02 Aug 2022 14:43:30: 3000000 INFO @ Tue, 02 Aug 2022 14:43:36: 1000000 INFO @ Tue, 02 Aug 2022 14:43:43: 6000000 INFO @ Tue, 02 Aug 2022 14:43:43: 4000000 INFO @ Tue, 02 Aug 2022 14:43:48: 2000000 INFO @ Tue, 02 Aug 2022 14:43:56: 5000000 INFO @ Tue, 02 Aug 2022 14:43:57: 7000000 INFO @ Tue, 02 Aug 2022 14:44:01: 3000000 INFO @ Tue, 02 Aug 2022 14:44:08: 6000000 INFO @ Tue, 02 Aug 2022 14:44:10: 8000000 INFO @ Tue, 02 Aug 2022 14:44:14: 4000000 INFO @ Tue, 02 Aug 2022 14:44:20: 7000000 INFO @ Tue, 02 Aug 2022 14:44:23: 9000000 INFO @ Tue, 02 Aug 2022 14:44:27: 5000000 INFO @ Tue, 02 Aug 2022 14:44:34: 8000000 INFO @ Tue, 02 Aug 2022 14:44:39: 10000000 INFO @ Tue, 02 Aug 2022 14:44:39: 6000000 INFO @ Tue, 02 Aug 2022 14:44:47: 9000000 INFO @ Tue, 02 Aug 2022 14:44:51: 7000000 INFO @ Tue, 02 Aug 2022 14:44:54: 11000000 INFO @ Tue, 02 Aug 2022 14:45:00: 10000000 INFO @ Tue, 02 Aug 2022 14:45:04: 8000000 INFO @ Tue, 02 Aug 2022 14:45:13: 12000000 INFO @ Tue, 02 Aug 2022 14:45:14: 11000000 INFO @ Tue, 02 Aug 2022 14:45:19: 9000000 INFO @ Tue, 02 Aug 2022 14:45:27: 12000000 INFO @ Tue, 02 Aug 2022 14:45:32: 10000000 INFO @ Tue, 02 Aug 2022 14:45:32: 13000000 INFO @ Tue, 02 Aug 2022 14:45:40: 13000000 INFO @ Tue, 02 Aug 2022 14:45:45: 11000000 INFO @ Tue, 02 Aug 2022 14:45:49: 14000000 INFO @ Tue, 02 Aug 2022 14:45:54: 14000000 INFO @ Tue, 02 Aug 2022 14:45:58: 12000000 INFO @ Tue, 02 Aug 2022 14:46:07: 15000000 INFO @ Tue, 02 Aug 2022 14:46:07: 15000000 INFO @ Tue, 02 Aug 2022 14:46:10: 13000000 INFO @ Tue, 02 Aug 2022 14:46:20: 16000000 INFO @ Tue, 02 Aug 2022 14:46:22: 14000000 INFO @ Tue, 02 Aug 2022 14:46:26: 16000000 INFO @ Tue, 02 Aug 2022 14:46:31: 17000000 INFO @ Tue, 02 Aug 2022 14:46:36: 15000000 INFO @ Tue, 02 Aug 2022 14:46:43: 18000000 INFO @ Tue, 02 Aug 2022 14:46:43: 17000000 INFO @ Tue, 02 Aug 2022 14:46:47: 16000000 INFO @ Tue, 02 Aug 2022 14:46:55: 19000000 INFO @ Tue, 02 Aug 2022 14:46:58: 17000000 INFO @ Tue, 02 Aug 2022 14:47:00: 18000000 INFO @ Tue, 02 Aug 2022 14:47:07: 20000000 INFO @ Tue, 02 Aug 2022 14:47:10: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:47:17: 19000000 INFO @ Tue, 02 Aug 2022 14:47:19: 21000000 INFO @ Tue, 02 Aug 2022 14:47:21: 19000000 INFO @ Tue, 02 Aug 2022 14:47:30: 22000000 INFO @ Tue, 02 Aug 2022 14:47:32: 20000000 INFO @ Tue, 02 Aug 2022 14:47:32: 20000000 INFO @ Tue, 02 Aug 2022 14:47:41: 23000000 INFO @ Tue, 02 Aug 2022 14:47:42: 21000000 INFO @ Tue, 02 Aug 2022 14:47:46: 21000000 INFO @ Tue, 02 Aug 2022 14:47:52: 22000000 INFO @ Tue, 02 Aug 2022 14:47:53: 24000000 INFO @ Tue, 02 Aug 2022 14:48:01: 22000000 INFO @ Tue, 02 Aug 2022 14:48:03: 23000000 INFO @ Tue, 02 Aug 2022 14:48:04: 25000000 INFO @ Tue, 02 Aug 2022 14:48:15: 24000000 INFO @ Tue, 02 Aug 2022 14:48:16: 23000000 INFO @ Tue, 02 Aug 2022 14:48:17: 26000000 INFO @ Tue, 02 Aug 2022 14:48:26: 25000000 INFO @ Tue, 02 Aug 2022 14:48:29: 27000000 INFO @ Tue, 02 Aug 2022 14:48:30: 24000000 INFO @ Tue, 02 Aug 2022 14:48:37: 26000000 INFO @ Tue, 02 Aug 2022 14:48:39: 28000000 INFO @ Tue, 02 Aug 2022 14:48:46: 25000000 INFO @ Tue, 02 Aug 2022 14:48:48: 27000000 INFO @ Tue, 02 Aug 2022 14:48:50: 29000000 INFO @ Tue, 02 Aug 2022 14:48:59: 28000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:49:01: 26000000 INFO @ Tue, 02 Aug 2022 14:49:02: 30000000 INFO @ Tue, 02 Aug 2022 14:49:11: 29000000 INFO @ Tue, 02 Aug 2022 14:49:15: 31000000 INFO @ Tue, 02 Aug 2022 14:49:17: 27000000 INFO @ Tue, 02 Aug 2022 14:49:23: 30000000 INFO @ Tue, 02 Aug 2022 14:49:27: 32000000 INFO @ Tue, 02 Aug 2022 14:49:33: 28000000 INFO @ Tue, 02 Aug 2022 14:49:35: 31000000 INFO @ Tue, 02 Aug 2022 14:49:40: 33000000 INFO @ Tue, 02 Aug 2022 14:49:47: 32000000 INFO @ Tue, 02 Aug 2022 14:49:49: 29000000 INFO @ Tue, 02 Aug 2022 14:49:53: 34000000 INFO @ Tue, 02 Aug 2022 14:49:59: 33000000 INFO @ Tue, 02 Aug 2022 14:50:04: 30000000 INFO @ Tue, 02 Aug 2022 14:50:05: 35000000 INFO @ Tue, 02 Aug 2022 14:50:10: 34000000 INFO @ Tue, 02 Aug 2022 14:50:17: 36000000 INFO @ Tue, 02 Aug 2022 14:50:20: 31000000 INFO @ Tue, 02 Aug 2022 14:50:21: 35000000 INFO @ Tue, 02 Aug 2022 14:50:29: 37000000 INFO @ Tue, 02 Aug 2022 14:50:32: 36000000 INFO @ Tue, 02 Aug 2022 14:50:35: 32000000 INFO @ Tue, 02 Aug 2022 14:50:42: 38000000 INFO @ Tue, 02 Aug 2022 14:50:43: 37000000 INFO @ Tue, 02 Aug 2022 14:50:47: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:50:47: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:50:47: #1 total tags in treatment: 38437136 INFO @ Tue, 02 Aug 2022 14:50:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:47: #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 14:50:48: #1 tags after filtering in treatment: 38437076 INFO @ Tue, 02 Aug 2022 14:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:48: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:51: 33000000 INFO @ Tue, 02 Aug 2022 14:50:52: #2 number of paired peaks: 537 WARNING @ Tue, 02 Aug 2022 14:50:52: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Tue, 02 Aug 2022 14:50:52: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:52: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:53: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:53: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:53: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 14:50:53: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 02 Aug 2022 14:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.10_model.r WARNING @ Tue, 02 Aug 2022 14:50:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:53: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 02 Aug 2022 14:50:53: #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 14:50:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:55: 38000000 INFO @ Tue, 02 Aug 2022 14:51:00: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:51:00: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:51:00: #1 total tags in treatment: 38437136 INFO @ Tue, 02 Aug 2022 14:51:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:00: #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 14:51:01: #1 tags after filtering in treatment: 38437076 INFO @ Tue, 02 Aug 2022 14:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:01: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:04: #2 number of paired peaks: 537 WARNING @ Tue, 02 Aug 2022 14:51:04: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Tue, 02 Aug 2022 14:51:04: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:05: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:05: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:05: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:05: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 14:51:05: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 02 Aug 2022 14:51:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.20_model.r WARNING @ Tue, 02 Aug 2022 14:51:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:51:05: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 02 Aug 2022 14:51:05: #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 14:51:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:51:06: 34000000 INFO @ Tue, 02 Aug 2022 14:51:20: 35000000 INFO @ Tue, 02 Aug 2022 14:51:34: 36000000 INFO @ Tue, 02 Aug 2022 14:51:48: 37000000 INFO @ Tue, 02 Aug 2022 14:52:03: 38000000 INFO @ Tue, 02 Aug 2022 14:52:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:52:09: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:52:09: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:52:09: #1 total tags in treatment: 38437136 INFO @ Tue, 02 Aug 2022 14:52:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:52:09: #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 14:52:11: #1 tags after filtering in treatment: 38437076 INFO @ Tue, 02 Aug 2022 14:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:52:11: #1 finished! INFO @ Tue, 02 Aug 2022 14:52:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:52:14: #2 number of paired peaks: 537 WARNING @ Tue, 02 Aug 2022 14:52:14: Fewer paired peaks (537) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 537 pairs to build model! INFO @ Tue, 02 Aug 2022 14:52:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:52:15: start X-correlation... INFO @ Tue, 02 Aug 2022 14:52:15: end of X-cor INFO @ Tue, 02 Aug 2022 14:52:15: #2 finished! INFO @ Tue, 02 Aug 2022 14:52:15: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 14:52:15: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 02 Aug 2022 14:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.05_model.r WARNING @ Tue, 02 Aug 2022 14:52:15: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:52:15: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 02 Aug 2022 14:52:15: #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 14:52:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:52:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:52:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:52:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:52:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.10_summits.bed INFO @ Tue, 02 Aug 2022 14:52:45: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.20_summits.bed INFO @ Tue, 02 Aug 2022 14:52:56: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:53:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:54:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:54:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:54:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148458/SRX14148458.05_summits.bed INFO @ Tue, 02 Aug 2022 14:54:08: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling