Job ID = 10166632 SRX = SRX7723718 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: 00:10:21 28473101 reads; of these: 28473101 (100.00%) were unpaired; of these: 2871026 (10.08%) aligned 0 times 20351893 (71.48%) aligned exactly 1 time 5250182 (18.44%) aligned >1 times 89.92% overall alignment rate Time searching: 00:10:21 Overall time: 00:10:21 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] 3695616 / 25602075 = 0.1443 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 @ Thu, 08 Oct 2020 22:15:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.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 @ Thu, 08 Oct 2020 22:15:28: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:15:28: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:15:34: 1000000 INFO @ Thu, 08 Oct 2020 22:15:40: 2000000 INFO @ Thu, 08 Oct 2020 22:15:45: 3000000 INFO @ Thu, 08 Oct 2020 22:15:51: 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 @ Thu, 08 Oct 2020 22:15:57: 5000000 INFO @ Thu, 08 Oct 2020 22:15:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.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 @ Thu, 08 Oct 2020 22:15:58: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:15:58: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:16:03: 6000000 INFO @ Thu, 08 Oct 2020 22:16:05: 1000000 INFO @ Thu, 08 Oct 2020 22:16:09: 7000000 INFO @ Thu, 08 Oct 2020 22:16:11: 2000000 INFO @ Thu, 08 Oct 2020 22:16:15: 8000000 INFO @ Thu, 08 Oct 2020 22:16:17: 3000000 INFO @ Thu, 08 Oct 2020 22:16:22: 9000000 INFO @ Thu, 08 Oct 2020 22:16:24: 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 @ Thu, 08 Oct 2020 22:16:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.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 @ Thu, 08 Oct 2020 22:16:28: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:16:28: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:16:28: 10000000 INFO @ Thu, 08 Oct 2020 22:16:30: 5000000 INFO @ Thu, 08 Oct 2020 22:16:34: 11000000 INFO @ Thu, 08 Oct 2020 22:16:34: 1000000 INFO @ Thu, 08 Oct 2020 22:16:36: 6000000 INFO @ Thu, 08 Oct 2020 22:16:40: 12000000 INFO @ Thu, 08 Oct 2020 22:16:41: 2000000 INFO @ Thu, 08 Oct 2020 22:16:43: 7000000 INFO @ Thu, 08 Oct 2020 22:16:47: 13000000 INFO @ Thu, 08 Oct 2020 22:16:47: 3000000 INFO @ Thu, 08 Oct 2020 22:16:49: 8000000 INFO @ Thu, 08 Oct 2020 22:16:53: 14000000 INFO @ Thu, 08 Oct 2020 22:16:53: 4000000 INFO @ Thu, 08 Oct 2020 22:16:56: 9000000 INFO @ Thu, 08 Oct 2020 22:16:59: 15000000 INFO @ Thu, 08 Oct 2020 22:17:00: 5000000 INFO @ Thu, 08 Oct 2020 22:17:02: 10000000 INFO @ Thu, 08 Oct 2020 22:17:05: 16000000 INFO @ Thu, 08 Oct 2020 22:17:06: 6000000 INFO @ Thu, 08 Oct 2020 22:17:09: 11000000 INFO @ Thu, 08 Oct 2020 22:17:11: 17000000 INFO @ Thu, 08 Oct 2020 22:17:13: 7000000 INFO @ Thu, 08 Oct 2020 22:17:15: 12000000 INFO @ Thu, 08 Oct 2020 22:17:18: 18000000 INFO @ Thu, 08 Oct 2020 22:17:19: 8000000 INFO @ Thu, 08 Oct 2020 22:17:21: 13000000 INFO @ Thu, 08 Oct 2020 22:17:24: 19000000 INFO @ Thu, 08 Oct 2020 22:17:25: 9000000 INFO @ Thu, 08 Oct 2020 22:17:28: 14000000 INFO @ Thu, 08 Oct 2020 22:17:30: 20000000 INFO @ Thu, 08 Oct 2020 22:17:32: 10000000 INFO @ Thu, 08 Oct 2020 22:17:34: 15000000 INFO @ Thu, 08 Oct 2020 22:17:37: 21000000 INFO @ Thu, 08 Oct 2020 22:17:38: 11000000 INFO @ Thu, 08 Oct 2020 22:17:40: 16000000 INFO @ Thu, 08 Oct 2020 22:17:43: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:17:43: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:17:43: #1 total tags in treatment: 21906459 INFO @ Thu, 08 Oct 2020 22:17:43: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:17:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:17:43: #1 tags after filtering in treatment: 21906273 INFO @ Thu, 08 Oct 2020 22:17:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:17:43: #1 finished! INFO @ Thu, 08 Oct 2020 22:17:43: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:17:44: 12000000 INFO @ Thu, 08 Oct 2020 22:17:45: #2 number of paired peaks: 519 WARNING @ Thu, 08 Oct 2020 22:17:45: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Thu, 08 Oct 2020 22:17:45: start model_add_line... INFO @ Thu, 08 Oct 2020 22:17:45: start X-correlation... INFO @ Thu, 08 Oct 2020 22:17:45: end of X-cor INFO @ Thu, 08 Oct 2020 22:17:45: #2 finished! INFO @ Thu, 08 Oct 2020 22:17:45: #2 predicted fragment length is 69 bps INFO @ Thu, 08 Oct 2020 22:17:45: #2 alternative fragment length(s) may be 3,69 bps INFO @ Thu, 08 Oct 2020 22:17:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.05_model.r WARNING @ Thu, 08 Oct 2020 22:17:45: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:17:45: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Thu, 08 Oct 2020 22:17:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:17:45: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:17:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:17:46: 17000000 INFO @ Thu, 08 Oct 2020 22:17:51: 13000000 INFO @ Thu, 08 Oct 2020 22:17:53: 18000000 INFO @ Thu, 08 Oct 2020 22:17:57: 14000000 INFO @ Thu, 08 Oct 2020 22:17:59: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 22:18:03: 15000000 INFO @ Thu, 08 Oct 2020 22:18:05: 20000000 INFO @ Thu, 08 Oct 2020 22:18:09: 16000000 INFO @ Thu, 08 Oct 2020 22:18:12: 21000000 INFO @ Thu, 08 Oct 2020 22:18:15: 17000000 INFO @ Thu, 08 Oct 2020 22:18:17: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:18:17: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:18:17: #1 total tags in treatment: 21906459 INFO @ Thu, 08 Oct 2020 22:18:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:18:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:18:18: #1 tags after filtering in treatment: 21906273 INFO @ Thu, 08 Oct 2020 22:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:18:18: #1 finished! INFO @ Thu, 08 Oct 2020 22:18:18: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:18:19: #2 number of paired peaks: 519 WARNING @ Thu, 08 Oct 2020 22:18:19: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Thu, 08 Oct 2020 22:18:19: start model_add_line... INFO @ Thu, 08 Oct 2020 22:18:20: start X-correlation... INFO @ Thu, 08 Oct 2020 22:18:20: end of X-cor INFO @ Thu, 08 Oct 2020 22:18:20: #2 finished! INFO @ Thu, 08 Oct 2020 22:18:20: #2 predicted fragment length is 69 bps INFO @ Thu, 08 Oct 2020 22:18:20: #2 alternative fragment length(s) may be 3,69 bps INFO @ Thu, 08 Oct 2020 22:18:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.10_model.r WARNING @ Thu, 08 Oct 2020 22:18:20: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:18:20: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Thu, 08 Oct 2020 22:18:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:18:20: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:18:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:18:22: 18000000 INFO @ Thu, 08 Oct 2020 22:18:24: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:18:27: 19000000 INFO @ Thu, 08 Oct 2020 22:18:33: 20000000 INFO @ Thu, 08 Oct 2020 22:18:39: 21000000 INFO @ Thu, 08 Oct 2020 22:18:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.05_peaks.xls INFO @ Thu, 08 Oct 2020 22:18:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:18:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.05_summits.bed INFO @ Thu, 08 Oct 2020 22:18:43: Done! INFO @ Thu, 08 Oct 2020 22:18:44: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 22:18:44: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 22:18:44: #1 total tags in treatment: 21906459 INFO @ Thu, 08 Oct 2020 22:18:44: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:18:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:18:45: #1 tags after filtering in treatment: 21906273 INFO @ Thu, 08 Oct 2020 22:18:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:18:45: #1 finished! INFO @ Thu, 08 Oct 2020 22:18:45: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:18:45: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (427 chroms): 2 millis pass2 - checking and writing primary data (3578 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:18:46: #2 number of paired peaks: 519 WARNING @ Thu, 08 Oct 2020 22:18:46: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Thu, 08 Oct 2020 22:18:46: start model_add_line... INFO @ Thu, 08 Oct 2020 22:18:46: start X-correlation... INFO @ Thu, 08 Oct 2020 22:18:46: end of X-cor INFO @ Thu, 08 Oct 2020 22:18:46: #2 finished! INFO @ Thu, 08 Oct 2020 22:18:46: #2 predicted fragment length is 69 bps INFO @ Thu, 08 Oct 2020 22:18:46: #2 alternative fragment length(s) may be 3,69 bps INFO @ Thu, 08 Oct 2020 22:18:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.20_model.r WARNING @ Thu, 08 Oct 2020 22:18:46: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:18:46: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Thu, 08 Oct 2020 22:18:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:18:46: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:18:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 22:18:57: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.10_peaks.xls INFO @ Thu, 08 Oct 2020 22:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.10_summits.bed INFO @ Thu, 08 Oct 2020 22:19:17: Done! pass1 - making usageList (341 chroms): 1 millis pass2 - checking and writing primary data (1657 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:19:24: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:19:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.20_peaks.xls INFO @ Thu, 08 Oct 2020 22:19:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:19:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723718/SRX7723718.20_summits.bed INFO @ Thu, 08 Oct 2020 22:19:43: Done! pass1 - making usageList (257 chroms): 1 millis pass2 - checking and writing primary data (835 records, 4 fields): 8 millis CompletedMACS2peakCalling