Job ID = 6529878 SRX = SRX5343142 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: 00:07:54 25511936 reads; of these: 25511936 (100.00%) were unpaired; of these: 1133017 (4.44%) aligned 0 times 21048021 (82.50%) aligned exactly 1 time 3330898 (13.06%) aligned >1 times 95.56% overall alignment rate Time searching: 00:07:54 Overall time: 00:07:54 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 12 files... [bam_rmdupse_core] 2638999 / 24378919 = 0.1082 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 03:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.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 03:19:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:05: 1000000 INFO @ Tue, 30 Jun 2020 03:20:10: 2000000 INFO @ Tue, 30 Jun 2020 03:20:16: 3000000 INFO @ Tue, 30 Jun 2020 03:20:21: 4000000 INFO @ Tue, 30 Jun 2020 03:20:27: 5000000 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 03:20:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.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 03:20:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:20:32: 6000000 INFO @ Tue, 30 Jun 2020 03:20:35: 1000000 INFO @ Tue, 30 Jun 2020 03:20:38: 7000000 INFO @ Tue, 30 Jun 2020 03:20:40: 2000000 INFO @ Tue, 30 Jun 2020 03:20:43: 8000000 INFO @ Tue, 30 Jun 2020 03:20:46: 3000000 INFO @ Tue, 30 Jun 2020 03:20:49: 9000000 INFO @ Tue, 30 Jun 2020 03:20:52: 4000000 INFO @ Tue, 30 Jun 2020 03:20:54: 10000000 INFO @ Tue, 30 Jun 2020 03:20:57: 5000000 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 03:20:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.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 03:20:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:20:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:21:00: 11000000 INFO @ Tue, 30 Jun 2020 03:21:03: 6000000 INFO @ Tue, 30 Jun 2020 03:21:06: 1000000 INFO @ Tue, 30 Jun 2020 03:21:06: 12000000 INFO @ Tue, 30 Jun 2020 03:21:09: 7000000 INFO @ Tue, 30 Jun 2020 03:21:12: 13000000 INFO @ Tue, 30 Jun 2020 03:21:12: 2000000 INFO @ Tue, 30 Jun 2020 03:21:15: 8000000 INFO @ Tue, 30 Jun 2020 03:21:18: 14000000 INFO @ Tue, 30 Jun 2020 03:21:18: 3000000 INFO @ Tue, 30 Jun 2020 03:21:21: 9000000 INFO @ Tue, 30 Jun 2020 03:21:23: 15000000 INFO @ Tue, 30 Jun 2020 03:21:24: 4000000 INFO @ Tue, 30 Jun 2020 03:21:26: 10000000 INFO @ Tue, 30 Jun 2020 03:21:29: 16000000 INFO @ Tue, 30 Jun 2020 03:21:30: 5000000 INFO @ Tue, 30 Jun 2020 03:21:32: 11000000 INFO @ Tue, 30 Jun 2020 03:21:35: 17000000 INFO @ Tue, 30 Jun 2020 03:21:35: 6000000 INFO @ Tue, 30 Jun 2020 03:21:38: 12000000 INFO @ Tue, 30 Jun 2020 03:21:40: 18000000 INFO @ Tue, 30 Jun 2020 03:21:41: 7000000 INFO @ Tue, 30 Jun 2020 03:21:44: 13000000 INFO @ Tue, 30 Jun 2020 03:21:46: 19000000 INFO @ Tue, 30 Jun 2020 03:21:47: 8000000 INFO @ Tue, 30 Jun 2020 03:21:49: 14000000 INFO @ Tue, 30 Jun 2020 03:21:52: 20000000 INFO @ Tue, 30 Jun 2020 03:21:52: 9000000 INFO @ Tue, 30 Jun 2020 03:21:55: 15000000 INFO @ Tue, 30 Jun 2020 03:21:58: 21000000 INFO @ Tue, 30 Jun 2020 03:21:58: 10000000 INFO @ Tue, 30 Jun 2020 03:22:00: 16000000 INFO @ Tue, 30 Jun 2020 03:22:03: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:22:03: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:22:03: #1 total tags in treatment: 21739920 INFO @ Tue, 30 Jun 2020 03:22:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:03: #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 03:22:03: #1 tags after filtering in treatment: 21739917 INFO @ Tue, 30 Jun 2020 03:22:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:03: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:03: 11000000 INFO @ Tue, 30 Jun 2020 03:22:05: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 03:22:05: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:05: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:05: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:05: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:05: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:22:05: #2 alternative fragment length(s) may be 2,67,546,572,582 bps INFO @ Tue, 30 Jun 2020 03:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.05_model.r WARNING @ Tue, 30 Jun 2020 03:22:05: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:22:05: #2 You may need to consider one of the other alternative d(s): 2,67,546,572,582 WARNING @ Tue, 30 Jun 2020 03:22:05: #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 03:22:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:06: 17000000 INFO @ Tue, 30 Jun 2020 03:22:09: 12000000 INFO @ Tue, 30 Jun 2020 03:22:11: 18000000 INFO @ Tue, 30 Jun 2020 03:22:14: 13000000 INFO @ Tue, 30 Jun 2020 03:22:17: 19000000 INFO @ Tue, 30 Jun 2020 03:22:20: 14000000 INFO @ Tue, 30 Jun 2020 03:22:22: 20000000 INFO @ Tue, 30 Jun 2020 03:22:25: 15000000 INFO @ Tue, 30 Jun 2020 03:22:28: 21000000 INFO @ Tue, 30 Jun 2020 03:22:30: 16000000 INFO @ Tue, 30 Jun 2020 03:22:32: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:22:32: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:22:32: #1 total tags in treatment: 21739920 INFO @ Tue, 30 Jun 2020 03:22:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:22:32: #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 03:22:33: #1 tags after filtering in treatment: 21739917 INFO @ Tue, 30 Jun 2020 03:22:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:22:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:22:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:22:34: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 03:22:34: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 03:22:34: start model_add_line... INFO @ Tue, 30 Jun 2020 03:22:34: start X-correlation... INFO @ Tue, 30 Jun 2020 03:22:34: end of X-cor INFO @ Tue, 30 Jun 2020 03:22:34: #2 finished! INFO @ Tue, 30 Jun 2020 03:22:34: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:22:34: #2 alternative fragment length(s) may be 2,67,546,572,582 bps INFO @ Tue, 30 Jun 2020 03:22:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.10_model.r WARNING @ Tue, 30 Jun 2020 03:22:34: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:22:34: #2 You may need to consider one of the other alternative d(s): 2,67,546,572,582 WARNING @ Tue, 30 Jun 2020 03:22:34: #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 03:22:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:22:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:22:35: 17000000 INFO @ Tue, 30 Jun 2020 03:22:40: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:22:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:46: 19000000 INFO @ Tue, 30 Jun 2020 03:22:51: 20000000 INFO @ Tue, 30 Jun 2020 03:22:56: 21000000 INFO @ Tue, 30 Jun 2020 03:23:01: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:23:01: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:23:01: #1 total tags in treatment: 21739920 INFO @ Tue, 30 Jun 2020 03:23:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:23:01: #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 03:23:01: #1 tags after filtering in treatment: 21739917 INFO @ Tue, 30 Jun 2020 03:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:23:01: #1 finished! INFO @ Tue, 30 Jun 2020 03:23:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:23:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:23:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.05_summits.bed INFO @ Tue, 30 Jun 2020 03:23:02: Done! pass1 - making usageList (324 chroms): 1 millis pass2 - checking and writing primary data (879 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:23:02: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 03:23:02: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 03:23:02: start model_add_line... INFO @ Tue, 30 Jun 2020 03:23:03: start X-correlation... INFO @ Tue, 30 Jun 2020 03:23:03: end of X-cor INFO @ Tue, 30 Jun 2020 03:23:03: #2 finished! INFO @ Tue, 30 Jun 2020 03:23:03: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:23:03: #2 alternative fragment length(s) may be 2,67,546,572,582 bps INFO @ Tue, 30 Jun 2020 03:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.20_model.r WARNING @ Tue, 30 Jun 2020 03:23:03: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:23:03: #2 You may need to consider one of the other alternative d(s): 2,67,546,572,582 WARNING @ Tue, 30 Jun 2020 03:23:03: #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 03:23:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:23:11: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:23:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.10_summits.bed INFO @ Tue, 30 Jun 2020 03:23:30: Done! pass1 - making usageList (178 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:23:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343142/SRX5343142.20_summits.bed INFO @ Tue, 30 Jun 2020 03:23:59: Done! pass1 - making usageList (102 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 3 millis CompletedMACS2peakCalling