Job ID = 6529801 SRX = SRX4933883 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: 00:04:13 14492663 reads; of these: 14492663 (100.00%) were unpaired; of these: 2489024 (17.17%) aligned 0 times 8088620 (55.81%) aligned exactly 1 time 3915019 (27.01%) aligned >1 times 82.83% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 3457721 / 12003639 = 0.2881 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 02:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.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 02:58:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:23: 1000000 INFO @ Tue, 30 Jun 2020 02:58:29: 2000000 INFO @ Tue, 30 Jun 2020 02:58:34: 3000000 INFO @ Tue, 30 Jun 2020 02:58:40: 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 @ Tue, 30 Jun 2020 02:58:46: 5000000 INFO @ Tue, 30 Jun 2020 02:58:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.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 02:58:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:52: 6000000 INFO @ Tue, 30 Jun 2020 02:58:54: 1000000 INFO @ Tue, 30 Jun 2020 02:58:59: 7000000 INFO @ Tue, 30 Jun 2020 02:59:00: 2000000 INFO @ Tue, 30 Jun 2020 02:59:05: 8000000 INFO @ Tue, 30 Jun 2020 02:59:06: 3000000 INFO @ Tue, 30 Jun 2020 02:59:09: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:59:09: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:59:09: #1 total tags in treatment: 8545918 INFO @ Tue, 30 Jun 2020 02:59:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:09: #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 02:59:09: #1 tags after filtering in treatment: 8545914 INFO @ Tue, 30 Jun 2020 02:59:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:09: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:10: #2 number of paired peaks: 1053 INFO @ Tue, 30 Jun 2020 02:59:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:10: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:59:10: #2 alternative fragment length(s) may be 2,55 bps INFO @ Tue, 30 Jun 2020 02:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.05_model.r WARNING @ Tue, 30 Jun 2020 02:59:10: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:59:10: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Tue, 30 Jun 2020 02:59:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:59:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:12: 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 02:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.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 02:59:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:19: 5000000 INFO @ Tue, 30 Jun 2020 02:59:24: 1000000 INFO @ Tue, 30 Jun 2020 02:59:25: 6000000 INFO @ Tue, 30 Jun 2020 02:59:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:59:30: 2000000 INFO @ Tue, 30 Jun 2020 02:59:32: 7000000 INFO @ Tue, 30 Jun 2020 02:59:36: 3000000 INFO @ Tue, 30 Jun 2020 02:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:59:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.05_summits.bed INFO @ Tue, 30 Jun 2020 02:59:38: Done! pass1 - making usageList (704 chroms): 2 millis pass2 - checking and writing primary data (2640 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:59:38: 8000000 INFO @ Tue, 30 Jun 2020 02:59:42: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:59:42: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:59:42: #1 total tags in treatment: 8545918 INFO @ Tue, 30 Jun 2020 02:59:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:42: #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 02:59:43: #1 tags after filtering in treatment: 8545914 INFO @ Tue, 30 Jun 2020 02:59:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:43: 4000000 INFO @ Tue, 30 Jun 2020 02:59:43: #2 number of paired peaks: 1053 INFO @ Tue, 30 Jun 2020 02:59:43: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:43: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:43: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:43: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:43: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:59:43: #2 alternative fragment length(s) may be 2,55 bps INFO @ Tue, 30 Jun 2020 02:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.10_model.r WARNING @ Tue, 30 Jun 2020 02:59:43: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:59:43: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Tue, 30 Jun 2020 02:59:43: #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 02:59:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:49: 5000000 INFO @ Tue, 30 Jun 2020 02:59:55: 6000000 INFO @ Tue, 30 Jun 2020 03:00:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:02: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:00:08: 8000000 INFO @ Tue, 30 Jun 2020 03:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.10_summits.bed INFO @ Tue, 30 Jun 2020 03:00:11: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (1957 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:00:12: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:00:12: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:00:12: #1 total tags in treatment: 8545918 INFO @ Tue, 30 Jun 2020 03:00:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:12: #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 03:00:12: #1 tags after filtering in treatment: 8545914 INFO @ Tue, 30 Jun 2020 03:00:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:12: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:13: #2 number of paired peaks: 1053 INFO @ Tue, 30 Jun 2020 03:00:13: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:13: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:13: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:13: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:13: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 03:00:13: #2 alternative fragment length(s) may be 2,55 bps INFO @ Tue, 30 Jun 2020 03:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.20_model.r WARNING @ Tue, 30 Jun 2020 03:00:13: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:00:13: #2 You may need to consider one of the other alternative d(s): 2,55 WARNING @ Tue, 30 Jun 2020 03:00:13: #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 03:00:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:00:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933883/SRX4933883.20_summits.bed INFO @ Tue, 30 Jun 2020 03:00:41: Done! pass1 - making usageList (373 chroms): 1 millis pass2 - checking and writing primary data (773 records, 4 fields): 12 millis CompletedMACS2peakCalling