Job ID = 6529237 SRX = SRX1084160 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: 00:05:55 21773844 reads; of these: 21773844 (100.00%) were unpaired; of these: 1095106 (5.03%) aligned 0 times 16020949 (73.58%) aligned exactly 1 time 4657789 (21.39%) aligned >1 times 94.97% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 1963974 / 20678738 = 0.0950 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 02:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.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 02:03:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:03:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:03:56: 1000000 INFO @ Tue, 30 Jun 2020 02:04:01: 2000000 INFO @ Tue, 30 Jun 2020 02:04:06: 3000000 INFO @ Tue, 30 Jun 2020 02:04:11: 4000000 INFO @ Tue, 30 Jun 2020 02:04:15: 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 02:04:20: 6000000 INFO @ Tue, 30 Jun 2020 02:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.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 02:04:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:25: 7000000 INFO @ Tue, 30 Jun 2020 02:04:27: 1000000 INFO @ Tue, 30 Jun 2020 02:04:31: 8000000 INFO @ Tue, 30 Jun 2020 02:04:34: 2000000 INFO @ Tue, 30 Jun 2020 02:04:36: 9000000 INFO @ Tue, 30 Jun 2020 02:04:40: 3000000 INFO @ Tue, 30 Jun 2020 02:04:41: 10000000 INFO @ Tue, 30 Jun 2020 02:04:46: 11000000 INFO @ Tue, 30 Jun 2020 02:04:46: 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 02:04:51: 12000000 INFO @ Tue, 30 Jun 2020 02:04:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.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 02:04:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:52: 5000000 INFO @ Tue, 30 Jun 2020 02:04:56: 13000000 INFO @ Tue, 30 Jun 2020 02:04:56: 1000000 INFO @ Tue, 30 Jun 2020 02:04:59: 6000000 INFO @ Tue, 30 Jun 2020 02:05:02: 14000000 INFO @ Tue, 30 Jun 2020 02:05:02: 2000000 INFO @ Tue, 30 Jun 2020 02:05:05: 7000000 INFO @ Tue, 30 Jun 2020 02:05:08: 3000000 INFO @ Tue, 30 Jun 2020 02:05:09: 15000000 INFO @ Tue, 30 Jun 2020 02:05:12: 8000000 INFO @ Tue, 30 Jun 2020 02:05:14: 4000000 INFO @ Tue, 30 Jun 2020 02:05:15: 16000000 INFO @ Tue, 30 Jun 2020 02:05:18: 9000000 INFO @ Tue, 30 Jun 2020 02:05:20: 5000000 INFO @ Tue, 30 Jun 2020 02:05:21: 17000000 INFO @ Tue, 30 Jun 2020 02:05:25: 10000000 INFO @ Tue, 30 Jun 2020 02:05:27: 6000000 INFO @ Tue, 30 Jun 2020 02:05:27: 18000000 INFO @ Tue, 30 Jun 2020 02:05:31: 11000000 INFO @ Tue, 30 Jun 2020 02:05:33: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:05:33: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:05:33: #1 total tags in treatment: 18714764 INFO @ Tue, 30 Jun 2020 02:05:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:33: #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 02:05:33: 7000000 INFO @ Tue, 30 Jun 2020 02:05:34: #1 tags after filtering in treatment: 18714693 INFO @ Tue, 30 Jun 2020 02:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:35: #2 number of paired peaks: 264 WARNING @ Tue, 30 Jun 2020 02:05:35: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:35: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 02:05:35: #2 alternative fragment length(s) may be 3,38,562 bps INFO @ Tue, 30 Jun 2020 02:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.05_model.r WARNING @ Tue, 30 Jun 2020 02:05:35: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:05:35: #2 You may need to consider one of the other alternative d(s): 3,38,562 WARNING @ Tue, 30 Jun 2020 02:05:35: #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 02:05:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:38: 12000000 INFO @ Tue, 30 Jun 2020 02:05:39: 8000000 INFO @ Tue, 30 Jun 2020 02:05:44: 13000000 INFO @ Tue, 30 Jun 2020 02:05:46: 9000000 INFO @ Tue, 30 Jun 2020 02:05:50: 14000000 INFO @ Tue, 30 Jun 2020 02:05:52: 10000000 INFO @ Tue, 30 Jun 2020 02:05:57: 15000000 INFO @ Tue, 30 Jun 2020 02:05:58: 11000000 INFO @ Tue, 30 Jun 2020 02:06:04: 16000000 INFO @ Tue, 30 Jun 2020 02:06:05: 12000000 INFO @ Tue, 30 Jun 2020 02:06:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:11: 17000000 INFO @ Tue, 30 Jun 2020 02:06:12: 13000000 INFO @ Tue, 30 Jun 2020 02:06:17: 18000000 INFO @ Tue, 30 Jun 2020 02:06:18: 14000000 INFO @ Tue, 30 Jun 2020 02:06:23: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:06:23: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:06:23: #1 total tags in treatment: 18714764 INFO @ Tue, 30 Jun 2020 02:06:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:23: #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 02:06:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.05_summits.bed INFO @ Tue, 30 Jun 2020 02:06:23: Done! INFO @ Tue, 30 Jun 2020 02:06:23: #1 tags after filtering in treatment: 18714693 INFO @ Tue, 30 Jun 2020 02:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:23: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (558 chroms): 2 millis pass2 - checking and writing primary data (2285 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:06:25: #2 number of paired peaks: 264 WARNING @ Tue, 30 Jun 2020 02:06:25: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:25: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 02:06:25: #2 alternative fragment length(s) may be 3,38,562 bps INFO @ Tue, 30 Jun 2020 02:06:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.10_model.r WARNING @ Tue, 30 Jun 2020 02:06:25: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:25: #2 You may need to consider one of the other alternative d(s): 3,38,562 WARNING @ Tue, 30 Jun 2020 02:06:25: #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 02:06:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:26: 15000000 INFO @ Tue, 30 Jun 2020 02:06:33: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:06:39: 17000000 INFO @ Tue, 30 Jun 2020 02:06:46: 18000000 INFO @ Tue, 30 Jun 2020 02:06:51: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:06:51: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:06:51: #1 total tags in treatment: 18714764 INFO @ Tue, 30 Jun 2020 02:06:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:51: #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 02:06:52: #1 tags after filtering in treatment: 18714693 INFO @ Tue, 30 Jun 2020 02:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:53: #2 number of paired peaks: 264 WARNING @ Tue, 30 Jun 2020 02:06:53: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:54: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:54: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:54: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 02:06:54: #2 alternative fragment length(s) may be 3,38,562 bps INFO @ Tue, 30 Jun 2020 02:06:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.20_model.r WARNING @ Tue, 30 Jun 2020 02:06:54: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:54: #2 You may need to consider one of the other alternative d(s): 3,38,562 WARNING @ Tue, 30 Jun 2020 02:06:54: #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 02:06:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.10_summits.bed INFO @ Tue, 30 Jun 2020 02:07:13: Done! pass1 - making usageList (430 chroms): 2 millis pass2 - checking and writing primary data (1575 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:07:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:07:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084160/SRX1084160.20_summits.bed INFO @ Tue, 30 Jun 2020 02:07:42: Done! pass1 - making usageList (187 chroms): 2 millis pass2 - checking and writing primary data (371 records, 4 fields): 11 millis CompletedMACS2peakCalling