Job ID = 6627534 SRX = SRX8521354 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: 00:08:09 52192245 reads; of these: 52192245 (100.00%) were unpaired; of these: 41356531 (79.24%) aligned 0 times 8007544 (15.34%) aligned exactly 1 time 2828170 (5.42%) aligned >1 times 20.76% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 2061272 / 10835714 = 0.1902 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, 14 Jul 2020 12:04:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.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, 14 Jul 2020 12:04:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:55: 1000000 INFO @ Tue, 14 Jul 2020 12:05:01: 2000000 INFO @ Tue, 14 Jul 2020 12:05:06: 3000000 INFO @ Tue, 14 Jul 2020 12:05:11: 4000000 INFO @ Tue, 14 Jul 2020 12:05:16: 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, 14 Jul 2020 12:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.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, 14 Jul 2020 12:05:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:05:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:05:21: 6000000 INFO @ Tue, 14 Jul 2020 12:05:26: 1000000 INFO @ Tue, 14 Jul 2020 12:05:27: 7000000 INFO @ Tue, 14 Jul 2020 12:05:31: 2000000 INFO @ Tue, 14 Jul 2020 12:05:33: 8000000 INFO @ Tue, 14 Jul 2020 12:05:37: 3000000 INFO @ Tue, 14 Jul 2020 12:05:37: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:05:37: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:05:37: #1 total tags in treatment: 8774442 INFO @ Tue, 14 Jul 2020 12:05:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:05:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:05:38: #1 tags after filtering in treatment: 8774276 INFO @ Tue, 14 Jul 2020 12:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:05:38: #1 finished! INFO @ Tue, 14 Jul 2020 12:05:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:05:38: #2 number of paired peaks: 448 WARNING @ Tue, 14 Jul 2020 12:05:38: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Tue, 14 Jul 2020 12:05:38: start model_add_line... INFO @ Tue, 14 Jul 2020 12:05:39: start X-correlation... INFO @ Tue, 14 Jul 2020 12:05:39: end of X-cor INFO @ Tue, 14 Jul 2020 12:05:39: #2 finished! INFO @ Tue, 14 Jul 2020 12:05:39: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 12:05:39: #2 alternative fragment length(s) may be 4,53,561 bps INFO @ Tue, 14 Jul 2020 12:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.05_model.r WARNING @ Tue, 14 Jul 2020 12:05:39: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:05:39: #2 You may need to consider one of the other alternative d(s): 4,53,561 WARNING @ Tue, 14 Jul 2020 12:05:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:05:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:05:42: 4000000 INFO @ Tue, 14 Jul 2020 12:05:48: 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, 14 Jul 2020 12:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.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, 14 Jul 2020 12:05:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:05:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:05:53: 6000000 INFO @ Tue, 14 Jul 2020 12:05:56: 1000000 INFO @ Tue, 14 Jul 2020 12:05:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:05:59: 7000000 INFO @ Tue, 14 Jul 2020 12:06:01: 2000000 INFO @ Tue, 14 Jul 2020 12:06:04: 8000000 INFO @ Tue, 14 Jul 2020 12:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.05_summits.bed INFO @ Tue, 14 Jul 2020 12:06:05: Done! pass1 - making usageList (303 chroms): 1 millis pass2 - checking and writing primary data (1391 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:06:07: 3000000 INFO @ Tue, 14 Jul 2020 12:06:09: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:06:09: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:06:09: #1 total tags in treatment: 8774442 INFO @ Tue, 14 Jul 2020 12:06:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:06:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:06:09: #1 tags after filtering in treatment: 8774276 INFO @ Tue, 14 Jul 2020 12:06:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:06:09: #1 finished! INFO @ Tue, 14 Jul 2020 12:06:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:06:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:06:10: #2 number of paired peaks: 448 WARNING @ Tue, 14 Jul 2020 12:06:10: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Tue, 14 Jul 2020 12:06:10: start model_add_line... INFO @ Tue, 14 Jul 2020 12:06:10: start X-correlation... INFO @ Tue, 14 Jul 2020 12:06:10: end of X-cor INFO @ Tue, 14 Jul 2020 12:06:10: #2 finished! INFO @ Tue, 14 Jul 2020 12:06:10: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 12:06:10: #2 alternative fragment length(s) may be 4,53,561 bps INFO @ Tue, 14 Jul 2020 12:06:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.10_model.r WARNING @ Tue, 14 Jul 2020 12:06:10: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:06:10: #2 You may need to consider one of the other alternative d(s): 4,53,561 WARNING @ Tue, 14 Jul 2020 12:06:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:06:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:06:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:06:13: 4000000 INFO @ Tue, 14 Jul 2020 12:06:18: 5000000 INFO @ Tue, 14 Jul 2020 12:06:23: 6000000 INFO @ Tue, 14 Jul 2020 12:06:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:06:29: 7000000 INFO @ Tue, 14 Jul 2020 12:06:34: 8000000 INFO @ Tue, 14 Jul 2020 12:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.10_summits.bed INFO @ Tue, 14 Jul 2020 12:06:36: Done! pass1 - making usageList (153 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:06:39: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:06:39: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:06:39: #1 total tags in treatment: 8774442 INFO @ Tue, 14 Jul 2020 12:06:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:06:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:06:39: #1 tags after filtering in treatment: 8774276 INFO @ Tue, 14 Jul 2020 12:06:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:06:39: #1 finished! INFO @ Tue, 14 Jul 2020 12:06:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:06:40: #2 number of paired peaks: 448 WARNING @ Tue, 14 Jul 2020 12:06:40: Fewer paired peaks (448) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 448 pairs to build model! INFO @ Tue, 14 Jul 2020 12:06:40: start model_add_line... INFO @ Tue, 14 Jul 2020 12:06:40: start X-correlation... INFO @ Tue, 14 Jul 2020 12:06:40: end of X-cor INFO @ Tue, 14 Jul 2020 12:06:40: #2 finished! INFO @ Tue, 14 Jul 2020 12:06:40: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 12:06:40: #2 alternative fragment length(s) may be 4,53,561 bps INFO @ Tue, 14 Jul 2020 12:06:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.20_model.r WARNING @ Tue, 14 Jul 2020 12:06:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:06:40: #2 You may need to consider one of the other alternative d(s): 4,53,561 WARNING @ Tue, 14 Jul 2020 12:06:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:06:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:06:40: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:06:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:07:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:07:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:07:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521354/SRX8521354.20_summits.bed INFO @ Tue, 14 Jul 2020 12:07:07: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 4 millis CompletedMACS2peakCalling