Job ID = 6529663 SRX = SRX3981614 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: 00:11:23 40008501 reads; of these: 40008501 (100.00%) were unpaired; of these: 1222615 (3.06%) aligned 0 times 30110434 (75.26%) aligned exactly 1 time 8675452 (21.68%) aligned >1 times 96.94% overall alignment rate Time searching: 00:11:23 Overall time: 00:11:23 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] 5140232 / 38785886 = 0.1325 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 02:55:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.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 02:55:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:55:35: 1000000 INFO @ Tue, 30 Jun 2020 02:55:42: 2000000 INFO @ Tue, 30 Jun 2020 02:55:50: 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 02:55:57: 4000000 INFO @ Tue, 30 Jun 2020 02:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.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 02:55:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:04: 5000000 INFO @ Tue, 30 Jun 2020 02:56:05: 1000000 INFO @ Tue, 30 Jun 2020 02:56:12: 6000000 INFO @ Tue, 30 Jun 2020 02:56:12: 2000000 INFO @ Tue, 30 Jun 2020 02:56:19: 3000000 INFO @ Tue, 30 Jun 2020 02:56:20: 7000000 INFO @ Tue, 30 Jun 2020 02:56:26: 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 02:56:28: 8000000 INFO @ Tue, 30 Jun 2020 02:56:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.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 02:56:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:33: 5000000 INFO @ Tue, 30 Jun 2020 02:56:36: 1000000 INFO @ Tue, 30 Jun 2020 02:56:36: 9000000 INFO @ Tue, 30 Jun 2020 02:56:40: 6000000 INFO @ Tue, 30 Jun 2020 02:56:42: 2000000 INFO @ Tue, 30 Jun 2020 02:56:44: 10000000 INFO @ Tue, 30 Jun 2020 02:56:47: 7000000 INFO @ Tue, 30 Jun 2020 02:56:49: 3000000 INFO @ Tue, 30 Jun 2020 02:56:52: 11000000 INFO @ Tue, 30 Jun 2020 02:56:54: 8000000 INFO @ Tue, 30 Jun 2020 02:56:57: 4000000 INFO @ Tue, 30 Jun 2020 02:56:59: 12000000 INFO @ Tue, 30 Jun 2020 02:57:01: 9000000 INFO @ Tue, 30 Jun 2020 02:57:04: 5000000 INFO @ Tue, 30 Jun 2020 02:57:07: 13000000 INFO @ Tue, 30 Jun 2020 02:57:08: 10000000 INFO @ Tue, 30 Jun 2020 02:57:11: 6000000 INFO @ Tue, 30 Jun 2020 02:57:15: 11000000 INFO @ Tue, 30 Jun 2020 02:57:15: 14000000 INFO @ Tue, 30 Jun 2020 02:57:18: 7000000 INFO @ Tue, 30 Jun 2020 02:57:22: 12000000 INFO @ Tue, 30 Jun 2020 02:57:23: 15000000 INFO @ Tue, 30 Jun 2020 02:57:25: 8000000 INFO @ Tue, 30 Jun 2020 02:57:29: 13000000 INFO @ Tue, 30 Jun 2020 02:57:31: 16000000 INFO @ Tue, 30 Jun 2020 02:57:32: 9000000 INFO @ Tue, 30 Jun 2020 02:57:36: 14000000 INFO @ Tue, 30 Jun 2020 02:57:39: 17000000 INFO @ Tue, 30 Jun 2020 02:57:39: 10000000 INFO @ Tue, 30 Jun 2020 02:57:43: 15000000 INFO @ Tue, 30 Jun 2020 02:57:46: 11000000 INFO @ Tue, 30 Jun 2020 02:57:46: 18000000 INFO @ Tue, 30 Jun 2020 02:57:50: 16000000 INFO @ Tue, 30 Jun 2020 02:57:53: 12000000 INFO @ Tue, 30 Jun 2020 02:57:54: 19000000 INFO @ Tue, 30 Jun 2020 02:57:57: 17000000 INFO @ Tue, 30 Jun 2020 02:58:00: 13000000 INFO @ Tue, 30 Jun 2020 02:58:02: 20000000 INFO @ Tue, 30 Jun 2020 02:58:04: 18000000 INFO @ Tue, 30 Jun 2020 02:58:07: 14000000 INFO @ Tue, 30 Jun 2020 02:58:10: 21000000 INFO @ Tue, 30 Jun 2020 02:58:11: 19000000 INFO @ Tue, 30 Jun 2020 02:58:14: 15000000 INFO @ Tue, 30 Jun 2020 02:58:17: 22000000 INFO @ Tue, 30 Jun 2020 02:58:18: 20000000 INFO @ Tue, 30 Jun 2020 02:58:21: 16000000 INFO @ Tue, 30 Jun 2020 02:58:25: 21000000 INFO @ Tue, 30 Jun 2020 02:58:25: 23000000 INFO @ Tue, 30 Jun 2020 02:58:28: 17000000 INFO @ Tue, 30 Jun 2020 02:58:32: 22000000 INFO @ Tue, 30 Jun 2020 02:58:33: 24000000 INFO @ Tue, 30 Jun 2020 02:58:35: 18000000 INFO @ Tue, 30 Jun 2020 02:58:39: 23000000 INFO @ Tue, 30 Jun 2020 02:58:41: 25000000 INFO @ Tue, 30 Jun 2020 02:58:42: 19000000 INFO @ Tue, 30 Jun 2020 02:58:46: 24000000 INFO @ Tue, 30 Jun 2020 02:58:49: 20000000 INFO @ Tue, 30 Jun 2020 02:58:49: 26000000 INFO @ Tue, 30 Jun 2020 02:58:53: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:58:56: 21000000 INFO @ Tue, 30 Jun 2020 02:58:57: 27000000 INFO @ Tue, 30 Jun 2020 02:59:00: 26000000 INFO @ Tue, 30 Jun 2020 02:59:03: 22000000 INFO @ Tue, 30 Jun 2020 02:59:05: 28000000 INFO @ Tue, 30 Jun 2020 02:59:07: 27000000 INFO @ Tue, 30 Jun 2020 02:59:10: 23000000 INFO @ Tue, 30 Jun 2020 02:59:13: 29000000 INFO @ Tue, 30 Jun 2020 02:59:14: 28000000 INFO @ Tue, 30 Jun 2020 02:59:17: 24000000 INFO @ Tue, 30 Jun 2020 02:59:21: 30000000 INFO @ Tue, 30 Jun 2020 02:59:21: 29000000 INFO @ Tue, 30 Jun 2020 02:59:24: 25000000 INFO @ Tue, 30 Jun 2020 02:59:28: 30000000 INFO @ Tue, 30 Jun 2020 02:59:29: 31000000 INFO @ Tue, 30 Jun 2020 02:59:31: 26000000 INFO @ Tue, 30 Jun 2020 02:59:35: 31000000 INFO @ Tue, 30 Jun 2020 02:59:37: 32000000 INFO @ Tue, 30 Jun 2020 02:59:38: 27000000 INFO @ Tue, 30 Jun 2020 02:59:43: 32000000 INFO @ Tue, 30 Jun 2020 02:59:45: 33000000 INFO @ Tue, 30 Jun 2020 02:59:46: 28000000 INFO @ Tue, 30 Jun 2020 02:59:50: 33000000 INFO @ Tue, 30 Jun 2020 02:59:51: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:59:51: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:59:51: #1 total tags in treatment: 33645654 INFO @ Tue, 30 Jun 2020 02:59:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:51: #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 02:59:52: #1 tags after filtering in treatment: 33645610 INFO @ Tue, 30 Jun 2020 02:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:53: 29000000 INFO @ Tue, 30 Jun 2020 02:59:54: #2 number of paired peaks: 153 WARNING @ Tue, 30 Jun 2020 02:59:54: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:54: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:54: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:54: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:54: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:54: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:59:54: #2 alternative fragment length(s) may be 2,50,109,123,517,546,591,598 bps INFO @ Tue, 30 Jun 2020 02:59:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.05_model.r WARNING @ Tue, 30 Jun 2020 02:59:54: #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 02:59:54: #2 You may need to consider one of the other alternative d(s): 2,50,109,123,517,546,591,598 WARNING @ Tue, 30 Jun 2020 02:59:54: #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 02:59:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:55: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:59:55: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:59:55: #1 total tags in treatment: 33645654 INFO @ Tue, 30 Jun 2020 02:59:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:55: #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 02:59:56: #1 tags after filtering in treatment: 33645610 INFO @ Tue, 30 Jun 2020 02:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:58: #2 number of paired peaks: 153 WARNING @ Tue, 30 Jun 2020 02:59:58: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:58: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:59:58: #2 alternative fragment length(s) may be 2,50,109,123,517,546,591,598 bps INFO @ Tue, 30 Jun 2020 02:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.10_model.r WARNING @ Tue, 30 Jun 2020 02:59:58: #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 02:59:58: #2 You may need to consider one of the other alternative d(s): 2,50,109,123,517,546,591,598 WARNING @ Tue, 30 Jun 2020 02:59:58: #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 02:59:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:59: 30000000 INFO @ Tue, 30 Jun 2020 03:00:05: 31000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:00:12: 32000000 INFO @ Tue, 30 Jun 2020 03:00:18: 33000000 INFO @ Tue, 30 Jun 2020 03:00:22: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:00:22: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:00:22: #1 total tags in treatment: 33645654 INFO @ Tue, 30 Jun 2020 03:00:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:22: #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 03:00:23: #1 tags after filtering in treatment: 33645610 INFO @ Tue, 30 Jun 2020 03:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:23: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:26: #2 number of paired peaks: 153 WARNING @ Tue, 30 Jun 2020 03:00:26: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:26: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:26: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:26: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:26: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:26: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:00:26: #2 alternative fragment length(s) may be 2,50,109,123,517,546,591,598 bps INFO @ Tue, 30 Jun 2020 03:00:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.20_model.r WARNING @ Tue, 30 Jun 2020 03:00:26: #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 03:00:26: #2 You may need to consider one of the other alternative d(s): 2,50,109,123,517,546,591,598 WARNING @ Tue, 30 Jun 2020 03:00:26: #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 03:00:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:00:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.10_summits.bed INFO @ Tue, 30 Jun 2020 03:01:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.05_summits.bed INFO @ Tue, 30 Jun 2020 03:01:31: Done! INFO @ Tue, 30 Jun 2020 03:01:31: Done! pass1 - making usageList (364 chroms): 1 millis pass2 - checking and writing primary data (1429 records, 4 fields): 14 millis CompletedMACS2peakCalling pass1 - making usageList (645 chroms): 2 millis pass2 - checking and writing primary data (3839 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981614/SRX3981614.20_summits.bed INFO @ Tue, 30 Jun 2020 03:02:00: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (382 records, 4 fields): 7 millis CompletedMACS2peakCalling