Job ID = 6626632 SRX = SRX7262567 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 103639389 spots for SRR10582194/SRR10582194.sra Written 103639389 spots for SRR10582194/SRR10582194.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626959 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:14 103639389 reads; of these: 103639389 (100.00%) were unpaired; of these: 92790605 (89.53%) aligned 0 times 7820492 (7.55%) aligned exactly 1 time 3028292 (2.92%) aligned >1 times 10.47% overall alignment rate Time searching: 00:17:14 Overall time: 00:17:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1824046 / 10848784 = 0.1681 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 08:30:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.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 08:30:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:30:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:30:56: 1000000 INFO @ Tue, 14 Jul 2020 08:31:01: 2000000 INFO @ Tue, 14 Jul 2020 08:31:07: 3000000 INFO @ Tue, 14 Jul 2020 08:31:12: 4000000 INFO @ Tue, 14 Jul 2020 08:31:18: 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 08:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.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 08:31:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:31:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:31:24: 6000000 INFO @ Tue, 14 Jul 2020 08:31:26: 1000000 INFO @ Tue, 14 Jul 2020 08:31:29: 7000000 INFO @ Tue, 14 Jul 2020 08:31:32: 2000000 INFO @ Tue, 14 Jul 2020 08:31:35: 8000000 INFO @ Tue, 14 Jul 2020 08:31:38: 3000000 INFO @ Tue, 14 Jul 2020 08:31:41: 9000000 INFO @ Tue, 14 Jul 2020 08:31:41: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:31:41: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:31:41: #1 total tags in treatment: 9024738 INFO @ Tue, 14 Jul 2020 08:31:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:31:41: #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 08:31:41: #1 tags after filtering in treatment: 9024738 INFO @ Tue, 14 Jul 2020 08:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:31:41: #1 finished! INFO @ Tue, 14 Jul 2020 08:31:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:31:42: #2 number of paired peaks: 1338 INFO @ Tue, 14 Jul 2020 08:31:42: start model_add_line... INFO @ Tue, 14 Jul 2020 08:31:42: start X-correlation... INFO @ Tue, 14 Jul 2020 08:31:42: end of X-cor INFO @ Tue, 14 Jul 2020 08:31:42: #2 finished! INFO @ Tue, 14 Jul 2020 08:31:42: #2 predicted fragment length is 76 bps INFO @ Tue, 14 Jul 2020 08:31:42: #2 alternative fragment length(s) may be 3,76,562,574,598 bps INFO @ Tue, 14 Jul 2020 08:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.05_model.r WARNING @ Tue, 14 Jul 2020 08:31:42: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:31:42: #2 You may need to consider one of the other alternative d(s): 3,76,562,574,598 WARNING @ Tue, 14 Jul 2020 08:31:42: #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 08:31:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:31:43: 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, 14 Jul 2020 08:31:49: 5000000 INFO @ Tue, 14 Jul 2020 08:31:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.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 08:31:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:31:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:31:54: 6000000 INFO @ Tue, 14 Jul 2020 08:31:57: 1000000 INFO @ Tue, 14 Jul 2020 08:31:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:32:00: 7000000 INFO @ Tue, 14 Jul 2020 08:32:03: 2000000 INFO @ Tue, 14 Jul 2020 08:32:06: 8000000 INFO @ Tue, 14 Jul 2020 08:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.05_summits.bed INFO @ Tue, 14 Jul 2020 08:32:09: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2036 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:32:10: 3000000 INFO @ Tue, 14 Jul 2020 08:32:11: 9000000 INFO @ Tue, 14 Jul 2020 08:32:12: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:32:12: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:32:12: #1 total tags in treatment: 9024738 INFO @ Tue, 14 Jul 2020 08:32:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:32:12: #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 08:32:12: #1 tags after filtering in treatment: 9024738 INFO @ Tue, 14 Jul 2020 08:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:32:12: #1 finished! INFO @ Tue, 14 Jul 2020 08:32:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:32:12: #2 number of paired peaks: 1338 INFO @ Tue, 14 Jul 2020 08:32:12: start model_add_line... INFO @ Tue, 14 Jul 2020 08:32:12: start X-correlation... INFO @ Tue, 14 Jul 2020 08:32:12: end of X-cor INFO @ Tue, 14 Jul 2020 08:32:12: #2 finished! INFO @ Tue, 14 Jul 2020 08:32:12: #2 predicted fragment length is 76 bps INFO @ Tue, 14 Jul 2020 08:32:12: #2 alternative fragment length(s) may be 3,76,562,574,598 bps INFO @ Tue, 14 Jul 2020 08:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.10_model.r WARNING @ Tue, 14 Jul 2020 08:32:12: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:32:12: #2 You may need to consider one of the other alternative d(s): 3,76,562,574,598 WARNING @ Tue, 14 Jul 2020 08:32:12: #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 08:32:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:32:16: 4000000 INFO @ Tue, 14 Jul 2020 08:32:22: 5000000 INFO @ Tue, 14 Jul 2020 08:32:28: 6000000 INFO @ Tue, 14 Jul 2020 08:32:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:32:34: 7000000 INFO @ Tue, 14 Jul 2020 08:32:40: 8000000 INFO @ Tue, 14 Jul 2020 08:32:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:32:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:32:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.10_summits.bed INFO @ Tue, 14 Jul 2020 08:32:41: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1252 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:32:47: 9000000 INFO @ Tue, 14 Jul 2020 08:32:47: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:32:47: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:32:47: #1 total tags in treatment: 9024738 INFO @ Tue, 14 Jul 2020 08:32:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:32:47: #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 08:32:47: #1 tags after filtering in treatment: 9024738 INFO @ Tue, 14 Jul 2020 08:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:32:47: #1 finished! INFO @ Tue, 14 Jul 2020 08:32:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:32:48: #2 number of paired peaks: 1338 INFO @ Tue, 14 Jul 2020 08:32:48: start model_add_line... INFO @ Tue, 14 Jul 2020 08:32:48: start X-correlation... INFO @ Tue, 14 Jul 2020 08:32:48: end of X-cor INFO @ Tue, 14 Jul 2020 08:32:48: #2 finished! INFO @ Tue, 14 Jul 2020 08:32:48: #2 predicted fragment length is 76 bps INFO @ Tue, 14 Jul 2020 08:32:48: #2 alternative fragment length(s) may be 3,76,562,574,598 bps INFO @ Tue, 14 Jul 2020 08:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.20_model.r WARNING @ Tue, 14 Jul 2020 08:32:48: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:32:48: #2 You may need to consider one of the other alternative d(s): 3,76,562,574,598 WARNING @ Tue, 14 Jul 2020 08:32:48: #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 08:32:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:32:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:33:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:33:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:33:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:33:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262567/SRX7262567.20_summits.bed INFO @ Tue, 14 Jul 2020 08:33:16: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (393 records, 4 fields): 2 millis CompletedMACS2peakCalling