Job ID = 6530110 SRX = SRX992689 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: 00:08:36 40401662 reads; of these: 40401662 (100.00%) were unpaired; of these: 13868858 (34.33%) aligned 0 times 19707247 (48.78%) aligned exactly 1 time 6825557 (16.89%) aligned >1 times 65.67% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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 12 files... [bam_rmdupse_core] 4223315 / 26532804 = 0.1592 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 03:33:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.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 03:33:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:33:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:33:37: 1000000 INFO @ Tue, 30 Jun 2020 03:33:43: 2000000 INFO @ Tue, 30 Jun 2020 03:33:49: 3000000 INFO @ Tue, 30 Jun 2020 03:33:55: 4000000 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 03:34:01: 5000000 INFO @ Tue, 30 Jun 2020 03:34:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.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 03:34:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:34:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:34:07: 6000000 INFO @ Tue, 30 Jun 2020 03:34:08: 1000000 INFO @ Tue, 30 Jun 2020 03:34:14: 7000000 INFO @ Tue, 30 Jun 2020 03:34:14: 2000000 INFO @ Tue, 30 Jun 2020 03:34:20: 8000000 INFO @ Tue, 30 Jun 2020 03:34:21: 3000000 INFO @ Tue, 30 Jun 2020 03:34:27: 9000000 INFO @ Tue, 30 Jun 2020 03:34:27: 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 03:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.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 03:34:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:34:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:34:34: 10000000 INFO @ Tue, 30 Jun 2020 03:34:34: 5000000 INFO @ Tue, 30 Jun 2020 03:34:38: 1000000 INFO @ Tue, 30 Jun 2020 03:34:40: 11000000 INFO @ Tue, 30 Jun 2020 03:34:41: 6000000 INFO @ Tue, 30 Jun 2020 03:34:45: 2000000 INFO @ Tue, 30 Jun 2020 03:34:47: 12000000 INFO @ Tue, 30 Jun 2020 03:34:47: 7000000 INFO @ Tue, 30 Jun 2020 03:34:51: 3000000 INFO @ Tue, 30 Jun 2020 03:34:54: 8000000 INFO @ Tue, 30 Jun 2020 03:34:54: 13000000 INFO @ Tue, 30 Jun 2020 03:34:58: 4000000 INFO @ Tue, 30 Jun 2020 03:35:00: 9000000 INFO @ Tue, 30 Jun 2020 03:35:01: 14000000 INFO @ Tue, 30 Jun 2020 03:35:05: 5000000 INFO @ Tue, 30 Jun 2020 03:35:07: 15000000 INFO @ Tue, 30 Jun 2020 03:35:07: 10000000 INFO @ Tue, 30 Jun 2020 03:35:11: 6000000 INFO @ Tue, 30 Jun 2020 03:35:14: 16000000 INFO @ Tue, 30 Jun 2020 03:35:14: 11000000 INFO @ Tue, 30 Jun 2020 03:35:18: 7000000 INFO @ Tue, 30 Jun 2020 03:35:20: 17000000 INFO @ Tue, 30 Jun 2020 03:35:21: 12000000 INFO @ Tue, 30 Jun 2020 03:35:25: 8000000 INFO @ Tue, 30 Jun 2020 03:35:27: 18000000 INFO @ Tue, 30 Jun 2020 03:35:27: 13000000 INFO @ Tue, 30 Jun 2020 03:35:31: 9000000 INFO @ Tue, 30 Jun 2020 03:35:34: 14000000 INFO @ Tue, 30 Jun 2020 03:35:34: 19000000 INFO @ Tue, 30 Jun 2020 03:35:38: 10000000 INFO @ Tue, 30 Jun 2020 03:35:40: 15000000 INFO @ Tue, 30 Jun 2020 03:35:41: 20000000 INFO @ Tue, 30 Jun 2020 03:35:45: 11000000 INFO @ Tue, 30 Jun 2020 03:35:47: 16000000 INFO @ Tue, 30 Jun 2020 03:35:47: 21000000 INFO @ Tue, 30 Jun 2020 03:35:51: 12000000 INFO @ Tue, 30 Jun 2020 03:35:53: 17000000 INFO @ Tue, 30 Jun 2020 03:35:54: 22000000 INFO @ Tue, 30 Jun 2020 03:35:56: #1 tag size is determined as 54 bps INFO @ Tue, 30 Jun 2020 03:35:56: #1 tag size = 54 INFO @ Tue, 30 Jun 2020 03:35:56: #1 total tags in treatment: 22309489 INFO @ Tue, 30 Jun 2020 03:35:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:35:56: #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 03:35:57: #1 tags after filtering in treatment: 22309488 INFO @ Tue, 30 Jun 2020 03:35:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:35:57: #1 finished! INFO @ Tue, 30 Jun 2020 03:35:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:35:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:35:58: #2 number of paired peaks: 247 WARNING @ Tue, 30 Jun 2020 03:35:58: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 30 Jun 2020 03:35:58: start model_add_line... INFO @ Tue, 30 Jun 2020 03:35:58: start X-correlation... INFO @ Tue, 30 Jun 2020 03:35:58: 13000000 INFO @ Tue, 30 Jun 2020 03:35:58: end of X-cor INFO @ Tue, 30 Jun 2020 03:35:58: #2 finished! INFO @ Tue, 30 Jun 2020 03:35:58: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:35:58: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 03:35:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.05_model.r WARNING @ Tue, 30 Jun 2020 03:35:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:35:58: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 03:35:58: #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 03:35:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:35:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:36:00: 18000000 INFO @ Tue, 30 Jun 2020 03:36:05: 14000000 INFO @ Tue, 30 Jun 2020 03:36:07: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:36:11: 15000000 INFO @ Tue, 30 Jun 2020 03:36:13: 20000000 INFO @ Tue, 30 Jun 2020 03:36:17: 16000000 INFO @ Tue, 30 Jun 2020 03:36:20: 21000000 INFO @ Tue, 30 Jun 2020 03:36:24: 17000000 INFO @ Tue, 30 Jun 2020 03:36:27: 22000000 INFO @ Tue, 30 Jun 2020 03:36:29: #1 tag size is determined as 54 bps INFO @ Tue, 30 Jun 2020 03:36:29: #1 tag size = 54 INFO @ Tue, 30 Jun 2020 03:36:29: #1 total tags in treatment: 22309489 INFO @ Tue, 30 Jun 2020 03:36:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:36:29: #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 03:36:29: #1 tags after filtering in treatment: 22309488 INFO @ Tue, 30 Jun 2020 03:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:36:29: #1 finished! INFO @ Tue, 30 Jun 2020 03:36:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:36:31: 18000000 INFO @ Tue, 30 Jun 2020 03:36:31: #2 number of paired peaks: 247 WARNING @ Tue, 30 Jun 2020 03:36:31: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 30 Jun 2020 03:36:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:36:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:36:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:36:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:36:31: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:36:31: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 03:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.10_model.r WARNING @ Tue, 30 Jun 2020 03:36:31: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:36:31: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 03:36:31: #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 03:36:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:36:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:36:37: 19000000 INFO @ Tue, 30 Jun 2020 03:36:43: 20000000 INFO @ Tue, 30 Jun 2020 03:36:49: 21000000 INFO @ Tue, 30 Jun 2020 03:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.05_summits.bed INFO @ Tue, 30 Jun 2020 03:36:54: Done! pass1 - making usageList (696 chroms): 2 millis pass2 - checking and writing primary data (3246 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:36:55: 22000000 INFO @ Tue, 30 Jun 2020 03:36:57: #1 tag size is determined as 54 bps INFO @ Tue, 30 Jun 2020 03:36:57: #1 tag size = 54 INFO @ Tue, 30 Jun 2020 03:36:57: #1 total tags in treatment: 22309489 INFO @ Tue, 30 Jun 2020 03:36:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:36:57: #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 03:36:58: #1 tags after filtering in treatment: 22309488 INFO @ Tue, 30 Jun 2020 03:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:36:58: #1 finished! INFO @ Tue, 30 Jun 2020 03:36:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:36:59: #2 number of paired peaks: 247 WARNING @ Tue, 30 Jun 2020 03:36:59: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Tue, 30 Jun 2020 03:36:59: start model_add_line... INFO @ Tue, 30 Jun 2020 03:36:59: start X-correlation... INFO @ Tue, 30 Jun 2020 03:36:59: end of X-cor INFO @ Tue, 30 Jun 2020 03:36:59: #2 finished! INFO @ Tue, 30 Jun 2020 03:36:59: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:36:59: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 03:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.20_model.r WARNING @ Tue, 30 Jun 2020 03:36:59: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:36:59: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 03:36:59: #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 03:36:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:36:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:37:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:37:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:37:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:37:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.10_summits.bed INFO @ Tue, 30 Jun 2020 03:37:26: Done! pass1 - making usageList (556 chroms): 1 millis pass2 - checking and writing primary data (1862 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:37:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:37:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:37:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:37:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX992689/SRX992689.20_summits.bed INFO @ Tue, 30 Jun 2020 03:37:56: Done! pass1 - making usageList (256 chroms): 1 millis pass2 - checking and writing primary data (530 records, 4 fields): 7 millis CompletedMACS2peakCalling