Job ID = 14168972 SRX = SRX8688980 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: 00:04:37 15362295 reads; of these: 15362295 (100.00%) were unpaired; of these: 538896 (3.51%) aligned 0 times 9881757 (64.32%) aligned exactly 1 time 4941642 (32.17%) aligned >1 times 96.49% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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 8 files... [bam_rmdupse_core] 2004692 / 14823399 = 0.1352 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 22:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.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 @ Fri, 10 Dec 2021 22:37:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:37:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:37:07: 1000000 INFO @ Fri, 10 Dec 2021 22:37:11: 2000000 INFO @ Fri, 10 Dec 2021 22:37:16: 3000000 INFO @ Fri, 10 Dec 2021 22:37:21: 4000000 INFO @ Fri, 10 Dec 2021 22:37:25: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 22:37:30: 6000000 INFO @ Fri, 10 Dec 2021 22:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.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 @ Fri, 10 Dec 2021 22:37:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:37:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:37:35: 7000000 INFO @ Fri, 10 Dec 2021 22:37:37: 1000000 INFO @ Fri, 10 Dec 2021 22:37:40: 8000000 INFO @ Fri, 10 Dec 2021 22:37:42: 2000000 INFO @ Fri, 10 Dec 2021 22:37:44: 9000000 INFO @ Fri, 10 Dec 2021 22:37:48: 3000000 INFO @ Fri, 10 Dec 2021 22:37:49: 10000000 INFO @ Fri, 10 Dec 2021 22:37:54: 4000000 INFO @ Fri, 10 Dec 2021 22:37:55: 11000000 BedGraph に変換中... INFO @ Fri, 10 Dec 2021 22:37:59: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 22:38:00: 12000000 INFO @ Fri, 10 Dec 2021 22:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.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 @ Fri, 10 Dec 2021 22:38:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:38:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:38:04: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:38:04: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:38:04: #1 total tags in treatment: 12818707 INFO @ Fri, 10 Dec 2021 22:38:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:38:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:38:04: #1 tags after filtering in treatment: 12818705 INFO @ Fri, 10 Dec 2021 22:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:38:04: #1 finished! INFO @ Fri, 10 Dec 2021 22:38:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:38:05: 6000000 INFO @ Fri, 10 Dec 2021 22:38:05: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 22:38:05: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 22:38:05: start model_add_line... INFO @ Fri, 10 Dec 2021 22:38:05: start X-correlation... INFO @ Fri, 10 Dec 2021 22:38:05: end of X-cor INFO @ Fri, 10 Dec 2021 22:38:05: #2 finished! INFO @ Fri, 10 Dec 2021 22:38:05: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 22:38:05: #2 alternative fragment length(s) may be 71 bps INFO @ Fri, 10 Dec 2021 22:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.05_model.r WARNING @ Fri, 10 Dec 2021 22:38:05: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:38:05: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Fri, 10 Dec 2021 22:38:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:38:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:38:06: 1000000 INFO @ Fri, 10 Dec 2021 22:38:11: 7000000 INFO @ Fri, 10 Dec 2021 22:38:11: 2000000 INFO @ Fri, 10 Dec 2021 22:38:16: 3000000 INFO @ Fri, 10 Dec 2021 22:38:16: 8000000 INFO @ Fri, 10 Dec 2021 22:38:21: 4000000 INFO @ Fri, 10 Dec 2021 22:38:22: 9000000 INFO @ Fri, 10 Dec 2021 22:38:25: 5000000 INFO @ Fri, 10 Dec 2021 22:38:27: 10000000 INFO @ Fri, 10 Dec 2021 22:38:30: 6000000 INFO @ Fri, 10 Dec 2021 22:38:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:38:33: 11000000 INFO @ Fri, 10 Dec 2021 22:38:35: 7000000 INFO @ Fri, 10 Dec 2021 22:38:39: 12000000 INFO @ Fri, 10 Dec 2021 22:38:40: 8000000 INFO @ Fri, 10 Dec 2021 22:38:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:38:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:38:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.05_summits.bed INFO @ Fri, 10 Dec 2021 22:38:42: Done! pass1 - making usageList (820 chroms): 1 millis pass2 - checking and writing primary data (3725 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:38:44: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:38:44: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:38:44: #1 total tags in treatment: 12818707 INFO @ Fri, 10 Dec 2021 22:38:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:38:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:38:44: #1 tags after filtering in treatment: 12818705 INFO @ Fri, 10 Dec 2021 22:38:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:38:44: #1 finished! INFO @ Fri, 10 Dec 2021 22:38:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:38:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:38:45: 9000000 INFO @ Fri, 10 Dec 2021 22:38:45: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 22:38:45: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 22:38:45: start model_add_line... INFO @ Fri, 10 Dec 2021 22:38:45: start X-correlation... INFO @ Fri, 10 Dec 2021 22:38:45: end of X-cor INFO @ Fri, 10 Dec 2021 22:38:45: #2 finished! INFO @ Fri, 10 Dec 2021 22:38:45: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 22:38:45: #2 alternative fragment length(s) may be 71 bps INFO @ Fri, 10 Dec 2021 22:38:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.10_model.r WARNING @ Fri, 10 Dec 2021 22:38:45: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:38:45: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Fri, 10 Dec 2021 22:38:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:38:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:38:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:38:50: 10000000 INFO @ Fri, 10 Dec 2021 22:38:55: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:38:59: 12000000 INFO @ Fri, 10 Dec 2021 22:39:04: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:39:04: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:39:04: #1 total tags in treatment: 12818707 INFO @ Fri, 10 Dec 2021 22:39:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:39:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:39:04: #1 tags after filtering in treatment: 12818705 INFO @ Fri, 10 Dec 2021 22:39:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:39:04: #1 finished! INFO @ Fri, 10 Dec 2021 22:39:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:39:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:39:05: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 22:39:05: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 22:39:05: start model_add_line... INFO @ Fri, 10 Dec 2021 22:39:05: start X-correlation... INFO @ Fri, 10 Dec 2021 22:39:05: end of X-cor INFO @ Fri, 10 Dec 2021 22:39:05: #2 finished! INFO @ Fri, 10 Dec 2021 22:39:05: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 22:39:05: #2 alternative fragment length(s) may be 71 bps INFO @ Fri, 10 Dec 2021 22:39:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.20_model.r WARNING @ Fri, 10 Dec 2021 22:39:05: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:39:05: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Fri, 10 Dec 2021 22:39:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 22:39:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:39:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:39:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:39:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:39:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:39:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.10_summits.bed INFO @ Fri, 10 Dec 2021 22:39:21: Done! pass1 - making usageList (514 chroms): 2 millis pass2 - checking and writing primary data (1534 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:39:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:39:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:39:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:39:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688980/SRX8688980.20_summits.bed INFO @ Fri, 10 Dec 2021 22:39:42: Done! pass1 - making usageList (314 chroms): 1 millis pass2 - checking and writing primary data (681 records, 4 fields): 10 millis CompletedMACS2peakCalling