Job ID = 6529369 SRX = SRX220302 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: 00:07:26 33925515 reads; of these: 33925515 (100.00%) were unpaired; of these: 1813748 (5.35%) aligned 0 times 21010695 (61.93%) aligned exactly 1 time 11101072 (32.72%) aligned >1 times 94.65% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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 8 files... [bam_rmdupse_core] 5444442 / 32111767 = 0.1695 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.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, 30 Jun 2020 02:43:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:43:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:01: 1000000 INFO @ Tue, 30 Jun 2020 02:44:06: 2000000 INFO @ Tue, 30 Jun 2020 02:44:11: 3000000 INFO @ Tue, 30 Jun 2020 02:44:16: 4000000 INFO @ Tue, 30 Jun 2020 02:44:22: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.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, 30 Jun 2020 02:44:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:27: 6000000 INFO @ Tue, 30 Jun 2020 02:44:32: 1000000 INFO @ Tue, 30 Jun 2020 02:44:34: 7000000 INFO @ Tue, 30 Jun 2020 02:44:39: 2000000 INFO @ Tue, 30 Jun 2020 02:44:41: 8000000 INFO @ Tue, 30 Jun 2020 02:44:46: 3000000 INFO @ Tue, 30 Jun 2020 02:44:47: 9000000 INFO @ Tue, 30 Jun 2020 02:44:53: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:44:54: 10000000 INFO @ Tue, 30 Jun 2020 02:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.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, 30 Jun 2020 02:44:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:00: 5000000 INFO @ Tue, 30 Jun 2020 02:45:01: 11000000 INFO @ Tue, 30 Jun 2020 02:45:02: 1000000 INFO @ Tue, 30 Jun 2020 02:45:07: 6000000 INFO @ Tue, 30 Jun 2020 02:45:07: 12000000 INFO @ Tue, 30 Jun 2020 02:45:10: 2000000 INFO @ Tue, 30 Jun 2020 02:45:14: 13000000 INFO @ Tue, 30 Jun 2020 02:45:14: 7000000 INFO @ Tue, 30 Jun 2020 02:45:17: 3000000 INFO @ Tue, 30 Jun 2020 02:45:21: 14000000 INFO @ Tue, 30 Jun 2020 02:45:21: 8000000 INFO @ Tue, 30 Jun 2020 02:45:25: 4000000 INFO @ Tue, 30 Jun 2020 02:45:28: 15000000 INFO @ Tue, 30 Jun 2020 02:45:28: 9000000 INFO @ Tue, 30 Jun 2020 02:45:32: 5000000 INFO @ Tue, 30 Jun 2020 02:45:35: 16000000 INFO @ Tue, 30 Jun 2020 02:45:36: 10000000 INFO @ Tue, 30 Jun 2020 02:45:39: 6000000 INFO @ Tue, 30 Jun 2020 02:45:41: 17000000 INFO @ Tue, 30 Jun 2020 02:45:43: 11000000 INFO @ Tue, 30 Jun 2020 02:45:47: 7000000 INFO @ Tue, 30 Jun 2020 02:45:48: 18000000 INFO @ Tue, 30 Jun 2020 02:45:50: 12000000 INFO @ Tue, 30 Jun 2020 02:45:54: 8000000 INFO @ Tue, 30 Jun 2020 02:45:55: 19000000 INFO @ Tue, 30 Jun 2020 02:45:57: 13000000 INFO @ Tue, 30 Jun 2020 02:46:01: 9000000 INFO @ Tue, 30 Jun 2020 02:46:02: 20000000 INFO @ Tue, 30 Jun 2020 02:46:04: 14000000 INFO @ Tue, 30 Jun 2020 02:46:08: 10000000 INFO @ Tue, 30 Jun 2020 02:46:09: 21000000 INFO @ Tue, 30 Jun 2020 02:46:11: 15000000 INFO @ Tue, 30 Jun 2020 02:46:16: 22000000 INFO @ Tue, 30 Jun 2020 02:46:16: 11000000 INFO @ Tue, 30 Jun 2020 02:46:18: 16000000 INFO @ Tue, 30 Jun 2020 02:46:23: 23000000 INFO @ Tue, 30 Jun 2020 02:46:23: 12000000 INFO @ Tue, 30 Jun 2020 02:46:25: 17000000 INFO @ Tue, 30 Jun 2020 02:46:30: 24000000 INFO @ Tue, 30 Jun 2020 02:46:31: 13000000 INFO @ Tue, 30 Jun 2020 02:46:33: 18000000 INFO @ Tue, 30 Jun 2020 02:46:37: 25000000 INFO @ Tue, 30 Jun 2020 02:46:38: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:46:40: 19000000 INFO @ Tue, 30 Jun 2020 02:46:44: 26000000 INFO @ Tue, 30 Jun 2020 02:46:46: 15000000 INFO @ Tue, 30 Jun 2020 02:46:47: 20000000 INFO @ Tue, 30 Jun 2020 02:46:49: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:46:49: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:46:49: #1 total tags in treatment: 26667325 INFO @ Tue, 30 Jun 2020 02:46:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:46:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:46:50: #1 tags after filtering in treatment: 26667292 INFO @ Tue, 30 Jun 2020 02:46:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:46:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:46:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:46:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:46:52: #2 number of paired peaks: 441 WARNING @ Tue, 30 Jun 2020 02:46:52: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Tue, 30 Jun 2020 02:46:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:46:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:46:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:46:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:46:52: #2 predicted fragment length is 40 bps INFO @ Tue, 30 Jun 2020 02:46:52: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 30 Jun 2020 02:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.05_model.r WARNING @ Tue, 30 Jun 2020 02:46:52: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:46:52: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 30 Jun 2020 02:46:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:46:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:46:53: 16000000 INFO @ Tue, 30 Jun 2020 02:46:54: 21000000 INFO @ Tue, 30 Jun 2020 02:47:00: 17000000 INFO @ Tue, 30 Jun 2020 02:47:01: 22000000 INFO @ Tue, 30 Jun 2020 02:47:08: 18000000 INFO @ Tue, 30 Jun 2020 02:47:09: 23000000 INFO @ Tue, 30 Jun 2020 02:47:15: 19000000 INFO @ Tue, 30 Jun 2020 02:47:16: 24000000 INFO @ Tue, 30 Jun 2020 02:47:23: 20000000 INFO @ Tue, 30 Jun 2020 02:47:23: 25000000 INFO @ Tue, 30 Jun 2020 02:47:30: 26000000 INFO @ Tue, 30 Jun 2020 02:47:30: 21000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:47:35: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:47:35: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:47:35: #1 total tags in treatment: 26667325 INFO @ Tue, 30 Jun 2020 02:47:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:47:35: #1 tags after filtering in treatment: 26667292 INFO @ Tue, 30 Jun 2020 02:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:47:37: 22000000 INFO @ Tue, 30 Jun 2020 02:47:37: #2 number of paired peaks: 441 WARNING @ Tue, 30 Jun 2020 02:47:37: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:37: #2 predicted fragment length is 40 bps INFO @ Tue, 30 Jun 2020 02:47:37: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 30 Jun 2020 02:47:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.10_model.r WARNING @ Tue, 30 Jun 2020 02:47:37: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:37: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 30 Jun 2020 02:47:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:47:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:43: 23000000 INFO @ Tue, 30 Jun 2020 02:47:48: 24000000 INFO @ Tue, 30 Jun 2020 02:47:54: 25000000 INFO @ Tue, 30 Jun 2020 02:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.05_summits.bed INFO @ Tue, 30 Jun 2020 02:47:58: Done! pass1 - making usageList (575 chroms): 2 millis pass2 - checking and writing primary data (5826 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:48:01: 26000000 INFO @ Tue, 30 Jun 2020 02:48:06: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:48:06: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:48:06: #1 total tags in treatment: 26667325 INFO @ Tue, 30 Jun 2020 02:48:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:48:06: #1 tags after filtering in treatment: 26667292 INFO @ Tue, 30 Jun 2020 02:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:06: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:08: #2 number of paired peaks: 441 WARNING @ Tue, 30 Jun 2020 02:48:08: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:08: #2 predicted fragment length is 40 bps INFO @ Tue, 30 Jun 2020 02:48:08: #2 alternative fragment length(s) may be 2,40 bps INFO @ Tue, 30 Jun 2020 02:48:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.20_model.r WARNING @ Tue, 30 Jun 2020 02:48:08: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:08: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Tue, 30 Jun 2020 02:48:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:48:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.10_summits.bed INFO @ Tue, 30 Jun 2020 02:48:45: Done! pass1 - making usageList (346 chroms): 2 millis pass2 - checking and writing primary data (1731 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:48:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220302/SRX220302.20_summits.bed INFO @ Tue, 30 Jun 2020 02:49:17: Done! pass1 - making usageList (174 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 6 millis CompletedMACS2peakCalling