Job ID = 6529694 SRX = SRX3981673 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: 00:10:38 39793952 reads; of these: 39793952 (100.00%) were unpaired; of these: 1109893 (2.79%) aligned 0 times 28685264 (72.08%) aligned exactly 1 time 9998795 (25.13%) aligned >1 times 97.21% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 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] 5254576 / 38684059 = 0.1358 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 02:54:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.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 02:54:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:54:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:54:47: 1000000 INFO @ Tue, 30 Jun 2020 02:54:55: 2000000 INFO @ Tue, 30 Jun 2020 02:55:04: 3000000 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 02:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.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 02:55:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:55:13: 4000000 INFO @ Tue, 30 Jun 2020 02:55:15: 1000000 INFO @ Tue, 30 Jun 2020 02:55:21: 5000000 INFO @ Tue, 30 Jun 2020 02:55:22: 2000000 INFO @ Tue, 30 Jun 2020 02:55:28: 3000000 INFO @ Tue, 30 Jun 2020 02:55:30: 6000000 INFO @ Tue, 30 Jun 2020 02:55:34: 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 02:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.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 02:55:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:55:40: 7000000 INFO @ Tue, 30 Jun 2020 02:55:41: 5000000 INFO @ Tue, 30 Jun 2020 02:55:48: 1000000 INFO @ Tue, 30 Jun 2020 02:55:48: 6000000 INFO @ Tue, 30 Jun 2020 02:55:49: 8000000 INFO @ Tue, 30 Jun 2020 02:55:55: 7000000 INFO @ Tue, 30 Jun 2020 02:55:57: 2000000 INFO @ Tue, 30 Jun 2020 02:55:58: 9000000 INFO @ Tue, 30 Jun 2020 02:56:02: 8000000 INFO @ Tue, 30 Jun 2020 02:56:06: 3000000 INFO @ Tue, 30 Jun 2020 02:56:06: 10000000 INFO @ Tue, 30 Jun 2020 02:56:10: 9000000 INFO @ Tue, 30 Jun 2020 02:56:15: 4000000 INFO @ Tue, 30 Jun 2020 02:56:15: 11000000 INFO @ Tue, 30 Jun 2020 02:56:19: 10000000 INFO @ Tue, 30 Jun 2020 02:56:23: 5000000 INFO @ Tue, 30 Jun 2020 02:56:23: 12000000 INFO @ Tue, 30 Jun 2020 02:56:27: 11000000 INFO @ Tue, 30 Jun 2020 02:56:31: 6000000 INFO @ Tue, 30 Jun 2020 02:56:32: 13000000 INFO @ Tue, 30 Jun 2020 02:56:36: 12000000 INFO @ Tue, 30 Jun 2020 02:56:40: 14000000 INFO @ Tue, 30 Jun 2020 02:56:40: 7000000 INFO @ Tue, 30 Jun 2020 02:56:45: 13000000 INFO @ Tue, 30 Jun 2020 02:56:49: 15000000 INFO @ Tue, 30 Jun 2020 02:56:49: 8000000 INFO @ Tue, 30 Jun 2020 02:56:54: 14000000 INFO @ Tue, 30 Jun 2020 02:56:57: 9000000 INFO @ Tue, 30 Jun 2020 02:56:57: 16000000 INFO @ Tue, 30 Jun 2020 02:57:03: 15000000 INFO @ Tue, 30 Jun 2020 02:57:05: 10000000 INFO @ Tue, 30 Jun 2020 02:57:05: 17000000 INFO @ Tue, 30 Jun 2020 02:57:12: 16000000 INFO @ Tue, 30 Jun 2020 02:57:13: 11000000 INFO @ Tue, 30 Jun 2020 02:57:13: 18000000 INFO @ Tue, 30 Jun 2020 02:57:21: 12000000 INFO @ Tue, 30 Jun 2020 02:57:21: 17000000 INFO @ Tue, 30 Jun 2020 02:57:22: 19000000 INFO @ Tue, 30 Jun 2020 02:57:29: 13000000 INFO @ Tue, 30 Jun 2020 02:57:30: 20000000 INFO @ Tue, 30 Jun 2020 02:57:30: 18000000 INFO @ Tue, 30 Jun 2020 02:57:37: 14000000 INFO @ Tue, 30 Jun 2020 02:57:39: 21000000 INFO @ Tue, 30 Jun 2020 02:57:39: 19000000 INFO @ Tue, 30 Jun 2020 02:57:46: 15000000 INFO @ Tue, 30 Jun 2020 02:57:47: 22000000 INFO @ Tue, 30 Jun 2020 02:57:48: 20000000 INFO @ Tue, 30 Jun 2020 02:57:54: 16000000 INFO @ Tue, 30 Jun 2020 02:57:55: 23000000 INFO @ Tue, 30 Jun 2020 02:57:58: 21000000 INFO @ Tue, 30 Jun 2020 02:58:02: 17000000 INFO @ Tue, 30 Jun 2020 02:58:03: 24000000 INFO @ Tue, 30 Jun 2020 02:58:07: 22000000 INFO @ Tue, 30 Jun 2020 02:58:10: 18000000 INFO @ Tue, 30 Jun 2020 02:58:10: 25000000 INFO @ Tue, 30 Jun 2020 02:58:16: 23000000 INFO @ Tue, 30 Jun 2020 02:58:17: 19000000 INFO @ Tue, 30 Jun 2020 02:58:18: 26000000 INFO @ Tue, 30 Jun 2020 02:58:25: 24000000 INFO @ Tue, 30 Jun 2020 02:58:25: 20000000 INFO @ Tue, 30 Jun 2020 02:58:26: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:58:33: 21000000 INFO @ Tue, 30 Jun 2020 02:58:33: 25000000 INFO @ Tue, 30 Jun 2020 02:58:34: 28000000 INFO @ Tue, 30 Jun 2020 02:58:41: 22000000 INFO @ Tue, 30 Jun 2020 02:58:42: 29000000 INFO @ Tue, 30 Jun 2020 02:58:42: 26000000 INFO @ Tue, 30 Jun 2020 02:58:48: 23000000 INFO @ Tue, 30 Jun 2020 02:58:50: 30000000 INFO @ Tue, 30 Jun 2020 02:58:50: 27000000 INFO @ Tue, 30 Jun 2020 02:58:57: 24000000 INFO @ Tue, 30 Jun 2020 02:58:58: 28000000 INFO @ Tue, 30 Jun 2020 02:58:58: 31000000 INFO @ Tue, 30 Jun 2020 02:59:05: 25000000 INFO @ Tue, 30 Jun 2020 02:59:06: 32000000 INFO @ Tue, 30 Jun 2020 02:59:07: 29000000 INFO @ Tue, 30 Jun 2020 02:59:12: 26000000 INFO @ Tue, 30 Jun 2020 02:59:14: 33000000 INFO @ Tue, 30 Jun 2020 02:59:15: 30000000 INFO @ Tue, 30 Jun 2020 02:59:18: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:59:18: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:59:18: #1 total tags in treatment: 33429483 INFO @ Tue, 30 Jun 2020 02:59:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:18: #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 02:59:19: #1 tags after filtering in treatment: 33429420 INFO @ Tue, 30 Jun 2020 02:59:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:19: 27000000 INFO @ Tue, 30 Jun 2020 02:59:21: #2 number of paired peaks: 160 WARNING @ Tue, 30 Jun 2020 02:59:21: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:21: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:59:21: #2 alternative fragment length(s) may be 2,46,554,557,590 bps INFO @ Tue, 30 Jun 2020 02:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.05_model.r WARNING @ Tue, 30 Jun 2020 02:59:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:59:21: #2 You may need to consider one of the other alternative d(s): 2,46,554,557,590 WARNING @ Tue, 30 Jun 2020 02:59:21: #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 02:59:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:24: 31000000 INFO @ Tue, 30 Jun 2020 02:59:26: 28000000 INFO @ Tue, 30 Jun 2020 02:59:33: 29000000 INFO @ Tue, 30 Jun 2020 02:59:33: 32000000 INFO @ Tue, 30 Jun 2020 02:59:39: 30000000 INFO @ Tue, 30 Jun 2020 02:59:42: 33000000 INFO @ Tue, 30 Jun 2020 02:59:45: 31000000 INFO @ Tue, 30 Jun 2020 02:59:46: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:59:46: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:59:46: #1 total tags in treatment: 33429483 INFO @ Tue, 30 Jun 2020 02:59:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:46: #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 02:59:47: #1 tags after filtering in treatment: 33429420 INFO @ Tue, 30 Jun 2020 02:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:49: #2 number of paired peaks: 160 WARNING @ Tue, 30 Jun 2020 02:59:49: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:49: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:49: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:49: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:49: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 02:59:49: #2 alternative fragment length(s) may be 2,46,554,557,590 bps INFO @ Tue, 30 Jun 2020 02:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.10_model.r WARNING @ Tue, 30 Jun 2020 02:59:49: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:59:49: #2 You may need to consider one of the other alternative d(s): 2,46,554,557,590 WARNING @ Tue, 30 Jun 2020 02:59:49: #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 02:59:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:52: 32000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:59:59: 33000000 INFO @ Tue, 30 Jun 2020 03:00:02: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:00:02: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:00:02: #1 total tags in treatment: 33429483 INFO @ Tue, 30 Jun 2020 03:00:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:02: #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 03:00:03: #1 tags after filtering in treatment: 33429420 INFO @ Tue, 30 Jun 2020 03:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:03: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:05: #2 number of paired peaks: 160 WARNING @ Tue, 30 Jun 2020 03:00:05: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:05: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:05: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:05: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:05: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:00:05: #2 alternative fragment length(s) may be 2,46,554,557,590 bps INFO @ Tue, 30 Jun 2020 03:00:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.20_model.r WARNING @ Tue, 30 Jun 2020 03:00:05: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:00:05: #2 You may need to consider one of the other alternative d(s): 2,46,554,557,590 WARNING @ Tue, 30 Jun 2020 03:00:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:00:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:00:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.05_summits.bed INFO @ Tue, 30 Jun 2020 03:00:35: Done! pass1 - making usageList (644 chroms): 2 millis pass2 - checking and writing primary data (3175 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:00:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.10_summits.bed INFO @ Tue, 30 Jun 2020 03:01:03: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (2054 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981673/SRX3981673.20_summits.bed INFO @ Tue, 30 Jun 2020 03:01:19: Done! pass1 - making usageList (257 chroms): 1 millis pass2 - checking and writing primary data (597 records, 4 fields): 16 millis CompletedMACS2peakCalling