Job ID = 6529857 SRX = SRX5287831 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: 00:09:26 23430975 reads; of these: 23430975 (100.00%) were unpaired; of these: 686051 (2.93%) aligned 0 times 17328996 (73.96%) aligned exactly 1 time 5415928 (23.11%) aligned >1 times 97.07% overall alignment rate Time searching: 00:09:26 Overall time: 00:09:26 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 12 files... [bam_rmdupse_core] 2798780 / 22744924 = 0.1231 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 03:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.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 03:10:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:47: 1000000 INFO @ Tue, 30 Jun 2020 03:10:54: 2000000 INFO @ Tue, 30 Jun 2020 03:11:01: 3000000 INFO @ Tue, 30 Jun 2020 03:11:07: 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 03:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.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 03:11:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:14: 5000000 INFO @ Tue, 30 Jun 2020 03:11:17: 1000000 INFO @ Tue, 30 Jun 2020 03:11:21: 6000000 INFO @ Tue, 30 Jun 2020 03:11:24: 2000000 INFO @ Tue, 30 Jun 2020 03:11:27: 7000000 INFO @ Tue, 30 Jun 2020 03:11:32: 3000000 INFO @ Tue, 30 Jun 2020 03:11:34: 8000000 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 03:11:39: 4000000 INFO @ Tue, 30 Jun 2020 03:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.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 03:11:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:41: 9000000 INFO @ Tue, 30 Jun 2020 03:11:46: 5000000 INFO @ Tue, 30 Jun 2020 03:11:47: 10000000 INFO @ Tue, 30 Jun 2020 03:11:47: 1000000 INFO @ Tue, 30 Jun 2020 03:11:53: 6000000 INFO @ Tue, 30 Jun 2020 03:11:54: 11000000 INFO @ Tue, 30 Jun 2020 03:11:54: 2000000 INFO @ Tue, 30 Jun 2020 03:12:00: 7000000 INFO @ Tue, 30 Jun 2020 03:12:01: 12000000 INFO @ Tue, 30 Jun 2020 03:12:01: 3000000 INFO @ Tue, 30 Jun 2020 03:12:07: 8000000 INFO @ Tue, 30 Jun 2020 03:12:07: 13000000 INFO @ Tue, 30 Jun 2020 03:12:08: 4000000 INFO @ Tue, 30 Jun 2020 03:12:14: 14000000 INFO @ Tue, 30 Jun 2020 03:12:14: 9000000 INFO @ Tue, 30 Jun 2020 03:12:15: 5000000 INFO @ Tue, 30 Jun 2020 03:12:21: 15000000 INFO @ Tue, 30 Jun 2020 03:12:21: 10000000 INFO @ Tue, 30 Jun 2020 03:12:22: 6000000 INFO @ Tue, 30 Jun 2020 03:12:28: 16000000 INFO @ Tue, 30 Jun 2020 03:12:28: 7000000 INFO @ Tue, 30 Jun 2020 03:12:28: 11000000 INFO @ Tue, 30 Jun 2020 03:12:35: 8000000 INFO @ Tue, 30 Jun 2020 03:12:35: 17000000 INFO @ Tue, 30 Jun 2020 03:12:36: 12000000 INFO @ Tue, 30 Jun 2020 03:12:42: 9000000 INFO @ Tue, 30 Jun 2020 03:12:42: 18000000 INFO @ Tue, 30 Jun 2020 03:12:43: 13000000 INFO @ Tue, 30 Jun 2020 03:12:48: 10000000 INFO @ Tue, 30 Jun 2020 03:12:49: 19000000 INFO @ Tue, 30 Jun 2020 03:12:50: 14000000 INFO @ Tue, 30 Jun 2020 03:12:55: 11000000 INFO @ Tue, 30 Jun 2020 03:12:56: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:12:56: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:12:56: #1 total tags in treatment: 19946144 INFO @ Tue, 30 Jun 2020 03:12:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:56: #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 03:12:56: #1 tags after filtering in treatment: 19946143 INFO @ Tue, 30 Jun 2020 03:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:56: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:57: 15000000 INFO @ Tue, 30 Jun 2020 03:12:58: #2 number of paired peaks: 329 WARNING @ Tue, 30 Jun 2020 03:12:58: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:58: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:58: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:58: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:58: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:58: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:12:58: #2 alternative fragment length(s) may be 3,66 bps INFO @ Tue, 30 Jun 2020 03:12:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.05_model.r WARNING @ Tue, 30 Jun 2020 03:12:58: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:58: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Tue, 30 Jun 2020 03:12:58: #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 03:12:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:02: 12000000 INFO @ Tue, 30 Jun 2020 03:13:04: 16000000 INFO @ Tue, 30 Jun 2020 03:13:09: 13000000 INFO @ Tue, 30 Jun 2020 03:13:12: 17000000 INFO @ Tue, 30 Jun 2020 03:13:15: 14000000 INFO @ Tue, 30 Jun 2020 03:13:19: 18000000 INFO @ Tue, 30 Jun 2020 03:13:22: 15000000 INFO @ Tue, 30 Jun 2020 03:13:26: 19000000 INFO @ Tue, 30 Jun 2020 03:13:29: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:13:33: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:13:33: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:13:33: #1 total tags in treatment: 19946144 INFO @ Tue, 30 Jun 2020 03:13:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:33: #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 03:13:34: #1 tags after filtering in treatment: 19946143 INFO @ Tue, 30 Jun 2020 03:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:34: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:35: #2 number of paired peaks: 329 WARNING @ Tue, 30 Jun 2020 03:13:35: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:35: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:13:35: #2 alternative fragment length(s) may be 3,66 bps INFO @ Tue, 30 Jun 2020 03:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.10_model.r WARNING @ Tue, 30 Jun 2020 03:13:35: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:35: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Tue, 30 Jun 2020 03:13:35: #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 03:13:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:35: 17000000 INFO @ Tue, 30 Jun 2020 03:13:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:42: 18000000 INFO @ Tue, 30 Jun 2020 03:13:49: 19000000 INFO @ Tue, 30 Jun 2020 03:13:55: #1 tag size is determined as 74 bps INFO @ Tue, 30 Jun 2020 03:13:55: #1 tag size = 74 INFO @ Tue, 30 Jun 2020 03:13:55: #1 total tags in treatment: 19946144 INFO @ Tue, 30 Jun 2020 03:13:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:55: #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 03:13:56: #1 tags after filtering in treatment: 19946143 INFO @ Tue, 30 Jun 2020 03:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:56: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:57: #2 number of paired peaks: 329 WARNING @ Tue, 30 Jun 2020 03:13:57: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:57: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:57: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:57: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:57: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:13:57: #2 alternative fragment length(s) may be 3,66 bps INFO @ Tue, 30 Jun 2020 03:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.20_model.r WARNING @ Tue, 30 Jun 2020 03:13:57: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:13:57: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Tue, 30 Jun 2020 03:13:57: #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 03:13:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.05_summits.bed INFO @ Tue, 30 Jun 2020 03:14:01: Done! pass1 - making usageList (682 chroms): 1 millis pass2 - checking and writing primary data (2344 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.10_summits.bed INFO @ Tue, 30 Jun 2020 03:14:37: Done! pass1 - making usageList (585 chroms): 1 millis pass2 - checking and writing primary data (1708 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:15:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:15:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:15:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5287831/SRX5287831.20_summits.bed INFO @ Tue, 30 Jun 2020 03:15:00: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (1034 records, 4 fields): 14 millis CompletedMACS2peakCalling