Job ID = 6529334 SRX = SRX1840077 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: 00:29:04 45897715 reads; of these: 45897715 (100.00%) were unpaired; of these: 1559093 (3.40%) aligned 0 times 29902317 (65.15%) aligned exactly 1 time 14436305 (31.45%) aligned >1 times 96.60% overall alignment rate Time searching: 00:29:04 Overall time: 00:29:04 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 20 files... [bam_rmdupse_core] 9632186 / 44338622 = 0.2172 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 02:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.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 02:33:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:30: 1000000 INFO @ Tue, 30 Jun 2020 02:33:37: 2000000 INFO @ Tue, 30 Jun 2020 02:33:43: 3000000 INFO @ Tue, 30 Jun 2020 02:33:50: 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 02:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.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 02:33:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:57: 5000000 INFO @ Tue, 30 Jun 2020 02:34:01: 1000000 INFO @ Tue, 30 Jun 2020 02:34:03: 6000000 INFO @ Tue, 30 Jun 2020 02:34:08: 2000000 INFO @ Tue, 30 Jun 2020 02:34:10: 7000000 INFO @ Tue, 30 Jun 2020 02:34:16: 3000000 INFO @ Tue, 30 Jun 2020 02:34:17: 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 02:34:23: 4000000 INFO @ Tue, 30 Jun 2020 02:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.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 02:34:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:34:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:34:24: 9000000 INFO @ Tue, 30 Jun 2020 02:34:30: 10000000 INFO @ Tue, 30 Jun 2020 02:34:30: 5000000 INFO @ Tue, 30 Jun 2020 02:34:31: 1000000 INFO @ Tue, 30 Jun 2020 02:34:37: 11000000 INFO @ Tue, 30 Jun 2020 02:34:38: 6000000 INFO @ Tue, 30 Jun 2020 02:34:39: 2000000 INFO @ Tue, 30 Jun 2020 02:34:44: 12000000 INFO @ Tue, 30 Jun 2020 02:34:45: 7000000 INFO @ Tue, 30 Jun 2020 02:34:46: 3000000 INFO @ Tue, 30 Jun 2020 02:34:50: 13000000 INFO @ Tue, 30 Jun 2020 02:34:53: 8000000 INFO @ Tue, 30 Jun 2020 02:34:54: 4000000 INFO @ Tue, 30 Jun 2020 02:34:57: 14000000 INFO @ Tue, 30 Jun 2020 02:35:00: 9000000 INFO @ Tue, 30 Jun 2020 02:35:02: 5000000 INFO @ Tue, 30 Jun 2020 02:35:04: 15000000 INFO @ Tue, 30 Jun 2020 02:35:07: 10000000 INFO @ Tue, 30 Jun 2020 02:35:09: 6000000 INFO @ Tue, 30 Jun 2020 02:35:11: 16000000 INFO @ Tue, 30 Jun 2020 02:35:15: 11000000 INFO @ Tue, 30 Jun 2020 02:35:17: 7000000 INFO @ Tue, 30 Jun 2020 02:35:17: 17000000 INFO @ Tue, 30 Jun 2020 02:35:22: 12000000 INFO @ Tue, 30 Jun 2020 02:35:24: 18000000 INFO @ Tue, 30 Jun 2020 02:35:24: 8000000 INFO @ Tue, 30 Jun 2020 02:35:29: 13000000 INFO @ Tue, 30 Jun 2020 02:35:30: 19000000 INFO @ Tue, 30 Jun 2020 02:35:32: 9000000 INFO @ Tue, 30 Jun 2020 02:35:36: 14000000 INFO @ Tue, 30 Jun 2020 02:35:37: 20000000 INFO @ Tue, 30 Jun 2020 02:35:39: 10000000 INFO @ Tue, 30 Jun 2020 02:35:43: 21000000 INFO @ Tue, 30 Jun 2020 02:35:43: 15000000 INFO @ Tue, 30 Jun 2020 02:35:46: 11000000 INFO @ Tue, 30 Jun 2020 02:35:50: 22000000 INFO @ Tue, 30 Jun 2020 02:35:51: 16000000 INFO @ Tue, 30 Jun 2020 02:35:54: 12000000 INFO @ Tue, 30 Jun 2020 02:35:56: 23000000 INFO @ Tue, 30 Jun 2020 02:35:58: 17000000 INFO @ Tue, 30 Jun 2020 02:36:01: 13000000 INFO @ Tue, 30 Jun 2020 02:36:02: 24000000 INFO @ Tue, 30 Jun 2020 02:36:05: 18000000 INFO @ Tue, 30 Jun 2020 02:36:08: 14000000 INFO @ Tue, 30 Jun 2020 02:36:09: 25000000 INFO @ Tue, 30 Jun 2020 02:36:12: 19000000 INFO @ Tue, 30 Jun 2020 02:36:15: 15000000 INFO @ Tue, 30 Jun 2020 02:36:16: 26000000 INFO @ Tue, 30 Jun 2020 02:36:19: 20000000 INFO @ Tue, 30 Jun 2020 02:36:22: 16000000 INFO @ Tue, 30 Jun 2020 02:36:23: 27000000 INFO @ Tue, 30 Jun 2020 02:36:27: 21000000 INFO @ Tue, 30 Jun 2020 02:36:29: 28000000 INFO @ Tue, 30 Jun 2020 02:36:30: 17000000 INFO @ Tue, 30 Jun 2020 02:36:34: 22000000 INFO @ Tue, 30 Jun 2020 02:36:36: 29000000 INFO @ Tue, 30 Jun 2020 02:36:37: 18000000 INFO @ Tue, 30 Jun 2020 02:36:41: 23000000 INFO @ Tue, 30 Jun 2020 02:36:43: 30000000 INFO @ Tue, 30 Jun 2020 02:36:44: 19000000 INFO @ Tue, 30 Jun 2020 02:36:48: 24000000 INFO @ Tue, 30 Jun 2020 02:36:50: 31000000 INFO @ Tue, 30 Jun 2020 02:36:52: 20000000 INFO @ Tue, 30 Jun 2020 02:36:55: 25000000 INFO @ Tue, 30 Jun 2020 02:36:57: 32000000 INFO @ Tue, 30 Jun 2020 02:36:59: 21000000 INFO @ Tue, 30 Jun 2020 02:37:03: 26000000 INFO @ Tue, 30 Jun 2020 02:37:04: 33000000 INFO @ Tue, 30 Jun 2020 02:37:06: 22000000 INFO @ Tue, 30 Jun 2020 02:37:10: 27000000 INFO @ Tue, 30 Jun 2020 02:37:11: 34000000 INFO @ Tue, 30 Jun 2020 02:37:14: 23000000 INFO @ Tue, 30 Jun 2020 02:37:16: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:37:16: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:37:16: #1 total tags in treatment: 34706436 INFO @ Tue, 30 Jun 2020 02:37:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:16: #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 02:37:17: #1 tags after filtering in treatment: 34706436 INFO @ Tue, 30 Jun 2020 02:37:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:18: 28000000 INFO @ Tue, 30 Jun 2020 02:37:20: #2 number of paired peaks: 156 WARNING @ Tue, 30 Jun 2020 02:37:20: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:20: #2 predicted fragment length is 72 bps INFO @ Tue, 30 Jun 2020 02:37:20: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 30 Jun 2020 02:37:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.05_model.r WARNING @ Tue, 30 Jun 2020 02:37:20: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:20: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 30 Jun 2020 02:37:20: #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 02:37:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:21: 24000000 INFO @ Tue, 30 Jun 2020 02:37:25: 29000000 INFO @ Tue, 30 Jun 2020 02:37:28: 25000000 INFO @ Tue, 30 Jun 2020 02:37:32: 30000000 INFO @ Tue, 30 Jun 2020 02:37:36: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:37:39: 31000000 INFO @ Tue, 30 Jun 2020 02:37:43: 27000000 INFO @ Tue, 30 Jun 2020 02:37:46: 32000000 INFO @ Tue, 30 Jun 2020 02:37:51: 28000000 INFO @ Tue, 30 Jun 2020 02:37:53: 33000000 INFO @ Tue, 30 Jun 2020 02:37:58: 29000000 INFO @ Tue, 30 Jun 2020 02:38:00: 34000000 INFO @ Tue, 30 Jun 2020 02:38:05: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:38:05: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:38:05: #1 total tags in treatment: 34706436 INFO @ Tue, 30 Jun 2020 02:38:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:38:05: #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 02:38:05: 30000000 INFO @ Tue, 30 Jun 2020 02:38:06: #1 tags after filtering in treatment: 34706436 INFO @ Tue, 30 Jun 2020 02:38:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:38:06: #1 finished! INFO @ Tue, 30 Jun 2020 02:38:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:38:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:38:08: #2 number of paired peaks: 156 WARNING @ Tue, 30 Jun 2020 02:38:08: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Tue, 30 Jun 2020 02:38:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:38:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:38:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:38:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:38:08: #2 predicted fragment length is 72 bps INFO @ Tue, 30 Jun 2020 02:38:08: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 30 Jun 2020 02:38:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.10_model.r WARNING @ Tue, 30 Jun 2020 02:38:08: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:38:08: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 30 Jun 2020 02:38:08: #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 02:38:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:38:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:38:12: 31000000 INFO @ Tue, 30 Jun 2020 02:38:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:20: 32000000 INFO @ Tue, 30 Jun 2020 02:38:27: 33000000 INFO @ Tue, 30 Jun 2020 02:38:34: 34000000 INFO @ Tue, 30 Jun 2020 02:38:39: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:38:39: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:38:39: #1 total tags in treatment: 34706436 INFO @ Tue, 30 Jun 2020 02:38:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:38:39: #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 02:38:40: #1 tags after filtering in treatment: 34706436 INFO @ Tue, 30 Jun 2020 02:38:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:38:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:38:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:38:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:38:42: #2 number of paired peaks: 156 WARNING @ Tue, 30 Jun 2020 02:38:42: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Tue, 30 Jun 2020 02:38:42: start model_add_line... INFO @ Tue, 30 Jun 2020 02:38:42: start X-correlation... INFO @ Tue, 30 Jun 2020 02:38:42: end of X-cor INFO @ Tue, 30 Jun 2020 02:38:42: #2 finished! INFO @ Tue, 30 Jun 2020 02:38:42: #2 predicted fragment length is 72 bps INFO @ Tue, 30 Jun 2020 02:38:42: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 30 Jun 2020 02:38:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.20_model.r WARNING @ Tue, 30 Jun 2020 02:38:42: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:38:42: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 30 Jun 2020 02:38:42: #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 02:38:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.05_summits.bed INFO @ Tue, 30 Jun 2020 02:38:44: Done! pass1 - making usageList (843 chroms): 1 millis pass2 - checking and writing primary data (3102 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:39:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.10_summits.bed INFO @ Tue, 30 Jun 2020 02:39:30: Done! pass1 - making usageList (752 chroms): 1 millis pass2 - checking and writing primary data (2177 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:39:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:40:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:40:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:40:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1840077/SRX1840077.20_summits.bed INFO @ Tue, 30 Jun 2020 02:40:04: Done! pass1 - making usageList (598 chroms): 1 millis pass2 - checking and writing primary data (1412 records, 4 fields): 17 millis CompletedMACS2peakCalling