Job ID = 6529662 SRX = SRX3981613 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: 00:11:54 41149889 reads; of these: 41149889 (100.00%) were unpaired; of these: 1179754 (2.87%) aligned 0 times 31296838 (76.06%) aligned exactly 1 time 8673297 (21.08%) aligned >1 times 97.13% overall alignment rate Time searching: 00:11:54 Overall time: 00:11:54 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] 5565064 / 39970135 = 0.1392 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 02:55:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.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 02:55:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:55:38: 1000000 INFO @ Tue, 30 Jun 2020 02:55:44: 2000000 INFO @ Tue, 30 Jun 2020 02:55:50: 3000000 INFO @ Tue, 30 Jun 2020 02:55:56: 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 02:56:01: 5000000 INFO @ Tue, 30 Jun 2020 02:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.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 02:56:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:08: 6000000 INFO @ Tue, 30 Jun 2020 02:56:10: 1000000 INFO @ Tue, 30 Jun 2020 02:56:15: 7000000 INFO @ Tue, 30 Jun 2020 02:56:17: 2000000 INFO @ Tue, 30 Jun 2020 02:56:21: 8000000 INFO @ Tue, 30 Jun 2020 02:56:24: 3000000 INFO @ Tue, 30 Jun 2020 02:56:28: 9000000 INFO @ Tue, 30 Jun 2020 02:56:30: 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 02:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.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 02:56:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:34: 10000000 INFO @ Tue, 30 Jun 2020 02:56:37: 5000000 INFO @ Tue, 30 Jun 2020 02:56:40: 1000000 INFO @ Tue, 30 Jun 2020 02:56:41: 11000000 INFO @ Tue, 30 Jun 2020 02:56:43: 6000000 INFO @ Tue, 30 Jun 2020 02:56:46: 2000000 INFO @ Tue, 30 Jun 2020 02:56:48: 12000000 INFO @ Tue, 30 Jun 2020 02:56:50: 7000000 INFO @ Tue, 30 Jun 2020 02:56:53: 3000000 INFO @ Tue, 30 Jun 2020 02:56:55: 13000000 INFO @ Tue, 30 Jun 2020 02:56:57: 8000000 INFO @ Tue, 30 Jun 2020 02:57:00: 4000000 INFO @ Tue, 30 Jun 2020 02:57:02: 14000000 INFO @ Tue, 30 Jun 2020 02:57:05: 9000000 INFO @ Tue, 30 Jun 2020 02:57:07: 5000000 INFO @ Tue, 30 Jun 2020 02:57:09: 15000000 INFO @ Tue, 30 Jun 2020 02:57:12: 10000000 INFO @ Tue, 30 Jun 2020 02:57:15: 6000000 INFO @ Tue, 30 Jun 2020 02:57:16: 16000000 INFO @ Tue, 30 Jun 2020 02:57:19: 11000000 INFO @ Tue, 30 Jun 2020 02:57:21: 7000000 INFO @ Tue, 30 Jun 2020 02:57:23: 17000000 INFO @ Tue, 30 Jun 2020 02:57:26: 12000000 INFO @ Tue, 30 Jun 2020 02:57:28: 8000000 INFO @ Tue, 30 Jun 2020 02:57:29: 18000000 INFO @ Tue, 30 Jun 2020 02:57:33: 13000000 INFO @ Tue, 30 Jun 2020 02:57:35: 9000000 INFO @ Tue, 30 Jun 2020 02:57:36: 19000000 INFO @ Tue, 30 Jun 2020 02:57:40: 14000000 INFO @ Tue, 30 Jun 2020 02:57:42: 10000000 INFO @ Tue, 30 Jun 2020 02:57:43: 20000000 INFO @ Tue, 30 Jun 2020 02:57:47: 15000000 INFO @ Tue, 30 Jun 2020 02:57:48: 11000000 INFO @ Tue, 30 Jun 2020 02:57:50: 21000000 INFO @ Tue, 30 Jun 2020 02:57:53: 16000000 INFO @ Tue, 30 Jun 2020 02:57:55: 12000000 INFO @ Tue, 30 Jun 2020 02:57:56: 22000000 INFO @ Tue, 30 Jun 2020 02:58:00: 17000000 INFO @ Tue, 30 Jun 2020 02:58:02: 13000000 INFO @ Tue, 30 Jun 2020 02:58:03: 23000000 INFO @ Tue, 30 Jun 2020 02:58:07: 18000000 INFO @ Tue, 30 Jun 2020 02:58:08: 14000000 INFO @ Tue, 30 Jun 2020 02:58:10: 24000000 INFO @ Tue, 30 Jun 2020 02:58:13: 19000000 INFO @ Tue, 30 Jun 2020 02:58:15: 15000000 INFO @ Tue, 30 Jun 2020 02:58:16: 25000000 INFO @ Tue, 30 Jun 2020 02:58:20: 20000000 INFO @ Tue, 30 Jun 2020 02:58:21: 16000000 INFO @ Tue, 30 Jun 2020 02:58:23: 26000000 INFO @ Tue, 30 Jun 2020 02:58:26: 21000000 INFO @ Tue, 30 Jun 2020 02:58:28: 17000000 INFO @ Tue, 30 Jun 2020 02:58:30: 27000000 INFO @ Tue, 30 Jun 2020 02:58:33: 22000000 INFO @ Tue, 30 Jun 2020 02:58:35: 18000000 INFO @ Tue, 30 Jun 2020 02:58:36: 28000000 INFO @ Tue, 30 Jun 2020 02:58:40: 23000000 INFO @ Tue, 30 Jun 2020 02:58:42: 19000000 INFO @ Tue, 30 Jun 2020 02:58:43: 29000000 INFO @ Tue, 30 Jun 2020 02:58:47: 24000000 INFO @ Tue, 30 Jun 2020 02:58:49: 20000000 INFO @ Tue, 30 Jun 2020 02:58:51: 30000000 INFO @ Tue, 30 Jun 2020 02:58:54: 25000000 INFO @ Tue, 30 Jun 2020 02:58:56: 21000000 INFO @ Tue, 30 Jun 2020 02:58:58: 31000000 INFO @ Tue, 30 Jun 2020 02:59:01: 26000000 INFO @ Tue, 30 Jun 2020 02:59:03: 22000000 INFO @ Tue, 30 Jun 2020 02:59:05: 32000000 INFO @ Tue, 30 Jun 2020 02:59:08: 27000000 INFO @ Tue, 30 Jun 2020 02:59:10: 23000000 INFO @ Tue, 30 Jun 2020 02:59:12: 33000000 INFO @ Tue, 30 Jun 2020 02:59:15: 28000000 INFO @ Tue, 30 Jun 2020 02:59:17: 24000000 INFO @ Tue, 30 Jun 2020 02:59:19: 34000000 INFO @ Tue, 30 Jun 2020 02:59:22: 29000000 INFO @ Tue, 30 Jun 2020 02:59:22: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:59:22: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:59:22: #1 total tags in treatment: 34405071 INFO @ Tue, 30 Jun 2020 02:59:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:22: #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 02:59:23: #1 tags after filtering in treatment: 34405019 INFO @ Tue, 30 Jun 2020 02:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:24: 25000000 INFO @ Tue, 30 Jun 2020 02:59:26: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 02:59:26: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:26: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:59:26: #2 alternative fragment length(s) may be 2,50,461,513 bps INFO @ Tue, 30 Jun 2020 02:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.05_model.r WARNING @ Tue, 30 Jun 2020 02:59:26: #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 02:59:26: #2 You may need to consider one of the other alternative d(s): 2,50,461,513 WARNING @ Tue, 30 Jun 2020 02:59:26: #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 02:59:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:29: 30000000 INFO @ Tue, 30 Jun 2020 02:59:32: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:59:36: 31000000 INFO @ Tue, 30 Jun 2020 02:59:39: 27000000 INFO @ Tue, 30 Jun 2020 02:59:44: 32000000 INFO @ Tue, 30 Jun 2020 02:59:46: 28000000 INFO @ Tue, 30 Jun 2020 02:59:51: 33000000 INFO @ Tue, 30 Jun 2020 02:59:53: 29000000 INFO @ Tue, 30 Jun 2020 02:59:58: 34000000 INFO @ Tue, 30 Jun 2020 03:00:01: 30000000 INFO @ Tue, 30 Jun 2020 03:00:02: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:00:02: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:00:02: #1 total tags in treatment: 34405071 INFO @ Tue, 30 Jun 2020 03:00:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:02: #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 03:00:02: #1 tags after filtering in treatment: 34405019 INFO @ Tue, 30 Jun 2020 03:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:02: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:05: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 03:00:05: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:05: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:05: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:05: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:05: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:00:05: #2 alternative fragment length(s) may be 2,50,461,513 bps INFO @ Tue, 30 Jun 2020 03:00:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.10_model.r WARNING @ Tue, 30 Jun 2020 03:00:05: #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 03:00:05: #2 You may need to consider one of the other alternative d(s): 2,50,461,513 WARNING @ Tue, 30 Jun 2020 03:00:05: #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 03:00:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:00:08: 31000000 INFO @ Tue, 30 Jun 2020 03:00:15: 32000000 INFO @ Tue, 30 Jun 2020 03:00:21: 33000000 INFO @ Tue, 30 Jun 2020 03:00:28: 34000000 INFO @ Tue, 30 Jun 2020 03:00:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:31: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:00:31: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:00:31: #1 total tags in treatment: 34405071 INFO @ Tue, 30 Jun 2020 03:00:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:31: #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 03:00:32: #1 tags after filtering in treatment: 34405019 INFO @ Tue, 30 Jun 2020 03:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:32: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:35: #2 number of paired peaks: 157 WARNING @ Tue, 30 Jun 2020 03:00:35: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:35: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:00:35: #2 alternative fragment length(s) may be 2,50,461,513 bps INFO @ Tue, 30 Jun 2020 03:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.20_model.r WARNING @ Tue, 30 Jun 2020 03:00:35: #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 03:00:35: #2 You may need to consider one of the other alternative d(s): 2,50,461,513 WARNING @ Tue, 30 Jun 2020 03:00:35: #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 03:00:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.05_summits.bed INFO @ Tue, 30 Jun 2020 03:01:03: Done! pass1 - making usageList (502 chroms): 2 millis pass2 - checking and writing primary data (3433 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:01:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.10_summits.bed INFO @ Tue, 30 Jun 2020 03:01:45: Done! pass1 - making usageList (287 chroms): 1 millis pass2 - checking and writing primary data (1390 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:02:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981613/SRX3981613.20_summits.bed INFO @ Tue, 30 Jun 2020 03:02:12: Done! pass1 - making usageList (141 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 6 millis CompletedMACS2peakCalling