Job ID = 6529196 SRX = SRX041380 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: 00:09:41 43573145 reads; of these: 43573145 (100.00%) were unpaired; of these: 974747 (2.24%) aligned 0 times 35384590 (81.21%) aligned exactly 1 time 7213808 (16.56%) aligned >1 times 97.76% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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] 13056043 / 42598398 = 0.3065 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 01:53:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.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 01:53:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:53:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:54:01: 1000000 INFO @ Tue, 30 Jun 2020 01:54:07: 2000000 INFO @ Tue, 30 Jun 2020 01:54:13: 3000000 INFO @ Tue, 30 Jun 2020 01:54:19: 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 01:54:25: 5000000 INFO @ Tue, 30 Jun 2020 01:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.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 01:54:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:54:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:54:32: 6000000 INFO @ Tue, 30 Jun 2020 01:54:32: 1000000 INFO @ Tue, 30 Jun 2020 01:54:38: 7000000 INFO @ Tue, 30 Jun 2020 01:54:38: 2000000 INFO @ Tue, 30 Jun 2020 01:54:44: 3000000 INFO @ Tue, 30 Jun 2020 01:54:44: 8000000 INFO @ Tue, 30 Jun 2020 01:54:50: 4000000 INFO @ Tue, 30 Jun 2020 01:54:51: 9000000 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 01:54:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.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 01:54:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:54:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:54:56: 5000000 INFO @ Tue, 30 Jun 2020 01:54:57: 10000000 INFO @ Tue, 30 Jun 2020 01:55:02: 1000000 INFO @ Tue, 30 Jun 2020 01:55:02: 6000000 INFO @ Tue, 30 Jun 2020 01:55:03: 11000000 INFO @ Tue, 30 Jun 2020 01:55:08: 2000000 INFO @ Tue, 30 Jun 2020 01:55:08: 7000000 INFO @ Tue, 30 Jun 2020 01:55:10: 12000000 INFO @ Tue, 30 Jun 2020 01:55:14: 3000000 INFO @ Tue, 30 Jun 2020 01:55:15: 8000000 INFO @ Tue, 30 Jun 2020 01:55:16: 13000000 INFO @ Tue, 30 Jun 2020 01:55:20: 4000000 INFO @ Tue, 30 Jun 2020 01:55:21: 9000000 INFO @ Tue, 30 Jun 2020 01:55:22: 14000000 INFO @ Tue, 30 Jun 2020 01:55:27: 5000000 INFO @ Tue, 30 Jun 2020 01:55:27: 10000000 INFO @ Tue, 30 Jun 2020 01:55:29: 15000000 INFO @ Tue, 30 Jun 2020 01:55:33: 11000000 INFO @ Tue, 30 Jun 2020 01:55:33: 6000000 INFO @ Tue, 30 Jun 2020 01:55:35: 16000000 INFO @ Tue, 30 Jun 2020 01:55:39: 12000000 INFO @ Tue, 30 Jun 2020 01:55:39: 7000000 INFO @ Tue, 30 Jun 2020 01:55:41: 17000000 INFO @ Tue, 30 Jun 2020 01:55:45: 13000000 INFO @ Tue, 30 Jun 2020 01:55:46: 8000000 INFO @ Tue, 30 Jun 2020 01:55:48: 18000000 INFO @ Tue, 30 Jun 2020 01:55:50: 14000000 INFO @ Tue, 30 Jun 2020 01:55:52: 9000000 INFO @ Tue, 30 Jun 2020 01:55:54: 19000000 INFO @ Tue, 30 Jun 2020 01:55:56: 15000000 INFO @ Tue, 30 Jun 2020 01:55:58: 10000000 INFO @ Tue, 30 Jun 2020 01:56:00: 20000000 INFO @ Tue, 30 Jun 2020 01:56:02: 16000000 INFO @ Tue, 30 Jun 2020 01:56:04: 11000000 INFO @ Tue, 30 Jun 2020 01:56:06: 21000000 INFO @ Tue, 30 Jun 2020 01:56:08: 17000000 INFO @ Tue, 30 Jun 2020 01:56:10: 12000000 INFO @ Tue, 30 Jun 2020 01:56:13: 22000000 INFO @ Tue, 30 Jun 2020 01:56:14: 18000000 INFO @ Tue, 30 Jun 2020 01:56:17: 13000000 INFO @ Tue, 30 Jun 2020 01:56:19: 23000000 INFO @ Tue, 30 Jun 2020 01:56:20: 19000000 INFO @ Tue, 30 Jun 2020 01:56:23: 14000000 INFO @ Tue, 30 Jun 2020 01:56:25: 24000000 INFO @ Tue, 30 Jun 2020 01:56:26: 20000000 INFO @ Tue, 30 Jun 2020 01:56:29: 15000000 INFO @ Tue, 30 Jun 2020 01:56:32: 21000000 INFO @ Tue, 30 Jun 2020 01:56:32: 25000000 INFO @ Tue, 30 Jun 2020 01:56:35: 16000000 INFO @ Tue, 30 Jun 2020 01:56:38: 22000000 INFO @ Tue, 30 Jun 2020 01:56:39: 26000000 INFO @ Tue, 30 Jun 2020 01:56:42: 17000000 INFO @ Tue, 30 Jun 2020 01:56:44: 23000000 INFO @ Tue, 30 Jun 2020 01:56:45: 27000000 INFO @ Tue, 30 Jun 2020 01:56:48: 18000000 INFO @ Tue, 30 Jun 2020 01:56:51: 24000000 INFO @ Tue, 30 Jun 2020 01:56:52: 28000000 INFO @ Tue, 30 Jun 2020 01:56:54: 19000000 INFO @ Tue, 30 Jun 2020 01:56:58: 25000000 INFO @ Tue, 30 Jun 2020 01:56:58: 29000000 INFO @ Tue, 30 Jun 2020 01:57:01: 20000000 INFO @ Tue, 30 Jun 2020 01:57:02: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:57:02: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:57:02: #1 total tags in treatment: 29542355 INFO @ Tue, 30 Jun 2020 01:57:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:02: #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 01:57:03: #1 tags after filtering in treatment: 29542354 INFO @ Tue, 30 Jun 2020 01:57:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:03: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:04: 26000000 INFO @ Tue, 30 Jun 2020 01:57:05: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 01:57:05: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:05: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:05: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:05: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:05: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:05: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 01:57:05: #2 alternative fragment length(s) may be 4,43,67,82,118 bps INFO @ Tue, 30 Jun 2020 01:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.05_model.r WARNING @ Tue, 30 Jun 2020 01:57:05: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:05: #2 You may need to consider one of the other alternative d(s): 4,43,67,82,118 WARNING @ Tue, 30 Jun 2020 01:57:05: #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 01:57:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:07: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:57:10: 27000000 INFO @ Tue, 30 Jun 2020 01:57:13: 22000000 INFO @ Tue, 30 Jun 2020 01:57:16: 28000000 INFO @ Tue, 30 Jun 2020 01:57:19: 23000000 INFO @ Tue, 30 Jun 2020 01:57:22: 29000000 INFO @ Tue, 30 Jun 2020 01:57:25: 24000000 INFO @ Tue, 30 Jun 2020 01:57:26: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:57:26: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:57:26: #1 total tags in treatment: 29542355 INFO @ Tue, 30 Jun 2020 01:57:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:26: #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 01:57:27: #1 tags after filtering in treatment: 29542354 INFO @ Tue, 30 Jun 2020 01:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:27: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:29: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 01:57:29: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:29: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:29: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:29: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:29: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:29: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 01:57:29: #2 alternative fragment length(s) may be 4,43,67,82,118 bps INFO @ Tue, 30 Jun 2020 01:57:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.10_model.r WARNING @ Tue, 30 Jun 2020 01:57:29: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:29: #2 You may need to consider one of the other alternative d(s): 4,43,67,82,118 WARNING @ Tue, 30 Jun 2020 01:57:29: #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 01:57:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:31: 25000000 INFO @ Tue, 30 Jun 2020 01:57:37: 26000000 INFO @ Tue, 30 Jun 2020 01:57:43: 27000000 INFO @ Tue, 30 Jun 2020 01:57:49: 28000000 INFO @ Tue, 30 Jun 2020 01:57:55: 29000000 INFO @ Tue, 30 Jun 2020 01:57:59: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:57:59: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:57:59: #1 total tags in treatment: 29542355 INFO @ Tue, 30 Jun 2020 01:57:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:59: #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 01:58:00: #1 tags after filtering in treatment: 29542354 INFO @ Tue, 30 Jun 2020 01:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:00: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:02: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 01:58:02: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:02: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:02: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:02: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:02: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:02: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 01:58:02: #2 alternative fragment length(s) may be 4,43,67,82,118 bps INFO @ Tue, 30 Jun 2020 01:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.20_model.r WARNING @ Tue, 30 Jun 2020 01:58:02: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:02: #2 You may need to consider one of the other alternative d(s): 4,43,67,82,118 WARNING @ Tue, 30 Jun 2020 01:58:02: #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 01:58:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:58:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.05_summits.bed INFO @ Tue, 30 Jun 2020 01:58:32: Done! pass1 - making usageList (512 chroms): 2 millis pass2 - checking and writing primary data (4516 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.10_summits.bed INFO @ Tue, 30 Jun 2020 01:58:55: Done! pass1 - making usageList (414 chroms): 1 millis pass2 - checking and writing primary data (2321 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:59:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041380/SRX041380.20_summits.bed INFO @ Tue, 30 Jun 2020 01:59:29: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 6 millis CompletedMACS2peakCalling