Job ID = 6626695 SRX = SRX7351010 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23400069 spots for SRR10673640/SRR10673640.sra Written 23400069 spots for SRR10673640/SRR10673640.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626979 ("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: 00:08:47 23400069 reads; of these: 23400069 (100.00%) were unpaired; of these: 698629 (2.99%) aligned 0 times 17996267 (76.91%) aligned exactly 1 time 4705173 (20.11%) aligned >1 times 97.01% overall alignment rate Time searching: 00:08:47 Overall time: 00:08:47 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 12 files... [bam_rmdupse_core] 3123707 / 22701440 = 0.1376 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 08:37:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.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 08:37:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:37:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:37:40: 1000000 INFO @ Tue, 14 Jul 2020 08:37:47: 2000000 INFO @ Tue, 14 Jul 2020 08:37:55: 3000000 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 08:38:01: 4000000 INFO @ Tue, 14 Jul 2020 08:38:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.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 08:38:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:38:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:38:09: 5000000 INFO @ Tue, 14 Jul 2020 08:38:10: 1000000 INFO @ Tue, 14 Jul 2020 08:38:16: 6000000 INFO @ Tue, 14 Jul 2020 08:38:17: 2000000 INFO @ Tue, 14 Jul 2020 08:38:23: 7000000 INFO @ Tue, 14 Jul 2020 08:38:24: 3000000 INFO @ Tue, 14 Jul 2020 08:38:30: 8000000 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 08:38:31: 4000000 INFO @ Tue, 14 Jul 2020 08:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.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 08:38:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:38:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:38:38: 9000000 INFO @ Tue, 14 Jul 2020 08:38:39: 5000000 INFO @ Tue, 14 Jul 2020 08:38:40: 1000000 INFO @ Tue, 14 Jul 2020 08:38:46: 10000000 INFO @ Tue, 14 Jul 2020 08:38:47: 6000000 INFO @ Tue, 14 Jul 2020 08:38:47: 2000000 INFO @ Tue, 14 Jul 2020 08:38:54: 11000000 INFO @ Tue, 14 Jul 2020 08:38:55: 7000000 INFO @ Tue, 14 Jul 2020 08:38:55: 3000000 INFO @ Tue, 14 Jul 2020 08:39:01: 12000000 INFO @ Tue, 14 Jul 2020 08:39:02: 8000000 INFO @ Tue, 14 Jul 2020 08:39:03: 4000000 INFO @ Tue, 14 Jul 2020 08:39:09: 13000000 INFO @ Tue, 14 Jul 2020 08:39:10: 5000000 INFO @ Tue, 14 Jul 2020 08:39:10: 9000000 INFO @ Tue, 14 Jul 2020 08:39:17: 14000000 INFO @ Tue, 14 Jul 2020 08:39:18: 6000000 INFO @ Tue, 14 Jul 2020 08:39:18: 10000000 INFO @ Tue, 14 Jul 2020 08:39:25: 15000000 INFO @ Tue, 14 Jul 2020 08:39:25: 7000000 INFO @ Tue, 14 Jul 2020 08:39:26: 11000000 INFO @ Tue, 14 Jul 2020 08:39:33: 8000000 INFO @ Tue, 14 Jul 2020 08:39:33: 16000000 INFO @ Tue, 14 Jul 2020 08:39:34: 12000000 INFO @ Tue, 14 Jul 2020 08:39:40: 9000000 INFO @ Tue, 14 Jul 2020 08:39:41: 17000000 INFO @ Tue, 14 Jul 2020 08:39:42: 13000000 INFO @ Tue, 14 Jul 2020 08:39:48: 10000000 INFO @ Tue, 14 Jul 2020 08:39:49: 18000000 INFO @ Tue, 14 Jul 2020 08:39:50: 14000000 INFO @ Tue, 14 Jul 2020 08:39:55: 11000000 INFO @ Tue, 14 Jul 2020 08:39:57: 19000000 INFO @ Tue, 14 Jul 2020 08:39:58: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:40:02: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:40:02: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:40:02: #1 total tags in treatment: 19577733 INFO @ Tue, 14 Jul 2020 08:40:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:40:02: #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 08:40:02: #1 tags after filtering in treatment: 19577733 INFO @ Tue, 14 Jul 2020 08:40:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:40:02: #1 finished! INFO @ Tue, 14 Jul 2020 08:40:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:40:03: 12000000 INFO @ Tue, 14 Jul 2020 08:40:03: #2 number of paired peaks: 1116 INFO @ Tue, 14 Jul 2020 08:40:03: start model_add_line... INFO @ Tue, 14 Jul 2020 08:40:03: start X-correlation... INFO @ Tue, 14 Jul 2020 08:40:03: end of X-cor INFO @ Tue, 14 Jul 2020 08:40:03: #2 finished! INFO @ Tue, 14 Jul 2020 08:40:03: #2 predicted fragment length is 87 bps INFO @ Tue, 14 Jul 2020 08:40:03: #2 alternative fragment length(s) may be 4,87 bps INFO @ Tue, 14 Jul 2020 08:40:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.05_model.r WARNING @ Tue, 14 Jul 2020 08:40:03: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:40:03: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Tue, 14 Jul 2020 08:40:03: #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 08:40:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:40:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:40:06: 16000000 INFO @ Tue, 14 Jul 2020 08:40:10: 13000000 INFO @ Tue, 14 Jul 2020 08:40:14: 17000000 INFO @ Tue, 14 Jul 2020 08:40:18: 14000000 INFO @ Tue, 14 Jul 2020 08:40:21: 18000000 INFO @ Tue, 14 Jul 2020 08:40:25: 15000000 INFO @ Tue, 14 Jul 2020 08:40:29: 19000000 INFO @ Tue, 14 Jul 2020 08:40:33: 16000000 INFO @ Tue, 14 Jul 2020 08:40:34: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:40:34: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:40:34: #1 total tags in treatment: 19577733 INFO @ Tue, 14 Jul 2020 08:40:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:40:34: #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 08:40:34: #1 tags after filtering in treatment: 19577733 INFO @ Tue, 14 Jul 2020 08:40:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:40:34: #1 finished! INFO @ Tue, 14 Jul 2020 08:40:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:40:36: #2 number of paired peaks: 1116 INFO @ Tue, 14 Jul 2020 08:40:36: start model_add_line... INFO @ Tue, 14 Jul 2020 08:40:36: start X-correlation... INFO @ Tue, 14 Jul 2020 08:40:36: end of X-cor INFO @ Tue, 14 Jul 2020 08:40:36: #2 finished! INFO @ Tue, 14 Jul 2020 08:40:36: #2 predicted fragment length is 87 bps INFO @ Tue, 14 Jul 2020 08:40:36: #2 alternative fragment length(s) may be 4,87 bps INFO @ Tue, 14 Jul 2020 08:40:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.10_model.r WARNING @ Tue, 14 Jul 2020 08:40:36: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:40:36: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Tue, 14 Jul 2020 08:40:36: #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 08:40:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:40:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:40:41: 17000000 INFO @ Tue, 14 Jul 2020 08:40:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:40:48: 18000000 INFO @ Tue, 14 Jul 2020 08:40:56: 19000000 INFO @ Tue, 14 Jul 2020 08:41:00: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:41:00: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:41:00: #1 total tags in treatment: 19577733 INFO @ Tue, 14 Jul 2020 08:41:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:41:00: #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 08:41:00: #1 tags after filtering in treatment: 19577733 INFO @ Tue, 14 Jul 2020 08:41:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:41:00: #1 finished! INFO @ Tue, 14 Jul 2020 08:41:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:41:02: #2 number of paired peaks: 1116 INFO @ Tue, 14 Jul 2020 08:41:02: start model_add_line... INFO @ Tue, 14 Jul 2020 08:41:02: start X-correlation... INFO @ Tue, 14 Jul 2020 08:41:02: end of X-cor INFO @ Tue, 14 Jul 2020 08:41:02: #2 finished! INFO @ Tue, 14 Jul 2020 08:41:02: #2 predicted fragment length is 87 bps INFO @ Tue, 14 Jul 2020 08:41:02: #2 alternative fragment length(s) may be 4,87 bps INFO @ Tue, 14 Jul 2020 08:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.20_model.r WARNING @ Tue, 14 Jul 2020 08:41:02: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:41:02: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Tue, 14 Jul 2020 08:41:02: #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 08:41:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:41:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:41:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:41:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:41:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.05_summits.bed INFO @ Tue, 14 Jul 2020 08:41:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10156 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:41:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.10_summits.bed INFO @ Tue, 14 Jul 2020 08:41:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5377 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:41:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351010/SRX7351010.20_summits.bed INFO @ Tue, 14 Jul 2020 08:42:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1627 records, 4 fields): 3 millis CompletedMACS2peakCalling