Job ID = 10166189 SRX = SRX7723710 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 45448402 spots for SRR11084666/SRR11084666.sra Written 45448402 spots for SRR11084666/SRR11084666.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166665 ("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: 00:19:04 45448402 reads; of these: 45448402 (100.00%) were unpaired; of these: 9252886 (20.36%) aligned 0 times 22290620 (49.05%) aligned exactly 1 time 13904896 (30.59%) aligned >1 times 79.64% overall alignment rate Time searching: 00:19:04 Overall time: 00:19:04 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 16 files... [bam_rmdupse_core] 15109345 / 36195516 = 0.4174 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 @ Thu, 08 Oct 2020 21:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.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 @ Thu, 08 Oct 2020 21:06:45: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:06:45: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:06:51: 1000000 INFO @ Thu, 08 Oct 2020 21:06:56: 2000000 INFO @ Thu, 08 Oct 2020 21:07:02: 3000000 INFO @ Thu, 08 Oct 2020 21:07:07: 4000000 INFO @ Thu, 08 Oct 2020 21:07:13: 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 @ Thu, 08 Oct 2020 21:07:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.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 @ Thu, 08 Oct 2020 21:07:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:07:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:07:19: 6000000 INFO @ Thu, 08 Oct 2020 21:07:22: 1000000 INFO @ Thu, 08 Oct 2020 21:07:25: 7000000 INFO @ Thu, 08 Oct 2020 21:07:29: 2000000 INFO @ Thu, 08 Oct 2020 21:07:31: 8000000 INFO @ Thu, 08 Oct 2020 21:07:36: 3000000 INFO @ Thu, 08 Oct 2020 21:07:37: 9000000 INFO @ Thu, 08 Oct 2020 21:07:43: 10000000 BedGraph に変換中... INFO @ Thu, 08 Oct 2020 21:07:43: 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 @ Thu, 08 Oct 2020 21:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.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 @ Thu, 08 Oct 2020 21:07:45: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:07:45: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:07:49: 11000000 INFO @ Thu, 08 Oct 2020 21:07:50: 5000000 INFO @ Thu, 08 Oct 2020 21:07:52: 1000000 INFO @ Thu, 08 Oct 2020 21:07:56: 12000000 INFO @ Thu, 08 Oct 2020 21:07:57: 6000000 INFO @ Thu, 08 Oct 2020 21:07:58: 2000000 INFO @ Thu, 08 Oct 2020 21:08:02: 13000000 INFO @ Thu, 08 Oct 2020 21:08:04: 7000000 INFO @ Thu, 08 Oct 2020 21:08:04: 3000000 INFO @ Thu, 08 Oct 2020 21:08:08: 14000000 INFO @ Thu, 08 Oct 2020 21:08:11: 4000000 INFO @ Thu, 08 Oct 2020 21:08:11: 8000000 INFO @ Thu, 08 Oct 2020 21:08:14: 15000000 INFO @ Thu, 08 Oct 2020 21:08:17: 5000000 INFO @ Thu, 08 Oct 2020 21:08:18: 9000000 INFO @ Thu, 08 Oct 2020 21:08:20: 16000000 INFO @ Thu, 08 Oct 2020 21:08:23: 6000000 INFO @ Thu, 08 Oct 2020 21:08:25: 10000000 INFO @ Thu, 08 Oct 2020 21:08:27: 17000000 INFO @ Thu, 08 Oct 2020 21:08:29: 7000000 INFO @ Thu, 08 Oct 2020 21:08:32: 11000000 INFO @ Thu, 08 Oct 2020 21:08:33: 18000000 INFO @ Thu, 08 Oct 2020 21:08:36: 8000000 INFO @ Thu, 08 Oct 2020 21:08:39: 12000000 INFO @ Thu, 08 Oct 2020 21:08:39: 19000000 INFO @ Thu, 08 Oct 2020 21:08:42: 9000000 INFO @ Thu, 08 Oct 2020 21:08:46: 20000000 INFO @ Thu, 08 Oct 2020 21:08:46: 13000000 INFO @ Thu, 08 Oct 2020 21:08:48: 10000000 INFO @ Thu, 08 Oct 2020 21:08:52: 21000000 INFO @ Thu, 08 Oct 2020 21:08:52: 14000000 INFO @ Thu, 08 Oct 2020 21:08:53: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:08:53: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:08:53: #1 total tags in treatment: 21086171 INFO @ Thu, 08 Oct 2020 21:08:53: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:08:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:08:53: #1 tags after filtering in treatment: 21086170 INFO @ Thu, 08 Oct 2020 21:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:08:53: #1 finished! INFO @ Thu, 08 Oct 2020 21:08:53: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:08:54: #2 number of paired peaks: 2770 INFO @ Thu, 08 Oct 2020 21:08:54: start model_add_line... INFO @ Thu, 08 Oct 2020 21:08:54: 11000000 INFO @ Thu, 08 Oct 2020 21:08:55: start X-correlation... INFO @ Thu, 08 Oct 2020 21:08:55: end of X-cor INFO @ Thu, 08 Oct 2020 21:08:55: #2 finished! INFO @ Thu, 08 Oct 2020 21:08:55: #2 predicted fragment length is 90 bps INFO @ Thu, 08 Oct 2020 21:08:55: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 08 Oct 2020 21:08:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05_model.r WARNING @ Thu, 08 Oct 2020 21:08:55: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:08:55: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 08 Oct 2020 21:08:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:08:55: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:08:59: 15000000 INFO @ Thu, 08 Oct 2020 21:09:01: 12000000 INFO @ Thu, 08 Oct 2020 21:09:06: 16000000 INFO @ Thu, 08 Oct 2020 21:09:07: 13000000 INFO @ Thu, 08 Oct 2020 21:09:13: 17000000 INFO @ Thu, 08 Oct 2020 21:09:13: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:09:19: 15000000 INFO @ Thu, 08 Oct 2020 21:09:20: 18000000 INFO @ Thu, 08 Oct 2020 21:09:25: 16000000 INFO @ Thu, 08 Oct 2020 21:09:27: 19000000 INFO @ Thu, 08 Oct 2020 21:09:32: 17000000 INFO @ Thu, 08 Oct 2020 21:09:34: 20000000 INFO @ Thu, 08 Oct 2020 21:09:34: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:09:38: 18000000 INFO @ Thu, 08 Oct 2020 21:09:41: 21000000 INFO @ Thu, 08 Oct 2020 21:09:41: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:09:41: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:09:41: #1 total tags in treatment: 21086171 INFO @ Thu, 08 Oct 2020 21:09:41: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:09:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:09:42: #1 tags after filtering in treatment: 21086170 INFO @ Thu, 08 Oct 2020 21:09:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:09:42: #1 finished! INFO @ Thu, 08 Oct 2020 21:09:42: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:09:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:09:43: #2 number of paired peaks: 2770 INFO @ Thu, 08 Oct 2020 21:09:43: start model_add_line... INFO @ Thu, 08 Oct 2020 21:09:43: start X-correlation... INFO @ Thu, 08 Oct 2020 21:09:43: end of X-cor INFO @ Thu, 08 Oct 2020 21:09:43: #2 finished! INFO @ Thu, 08 Oct 2020 21:09:43: #2 predicted fragment length is 90 bps INFO @ Thu, 08 Oct 2020 21:09:43: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 08 Oct 2020 21:09:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10_model.r WARNING @ Thu, 08 Oct 2020 21:09:43: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:09:43: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 08 Oct 2020 21:09:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:09:43: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:09:44: 19000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:09:50: 20000000 INFO @ Thu, 08 Oct 2020 21:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05_summits.bed INFO @ Thu, 08 Oct 2020 21:09:56: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (25349 records, 4 fields): 23 millis INFO @ Thu, 08 Oct 2020 21:09:56: 21000000 CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:09:57: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:09:57: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:09:57: #1 total tags in treatment: 21086171 INFO @ Thu, 08 Oct 2020 21:09:57: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:09:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:09:57: #1 tags after filtering in treatment: 21086170 INFO @ Thu, 08 Oct 2020 21:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:09:57: #1 finished! INFO @ Thu, 08 Oct 2020 21:09:57: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:09:59: #2 number of paired peaks: 2770 INFO @ Thu, 08 Oct 2020 21:09:59: start model_add_line... INFO @ Thu, 08 Oct 2020 21:09:59: start X-correlation... INFO @ Thu, 08 Oct 2020 21:09:59: end of X-cor INFO @ Thu, 08 Oct 2020 21:09:59: #2 finished! INFO @ Thu, 08 Oct 2020 21:09:59: #2 predicted fragment length is 90 bps INFO @ Thu, 08 Oct 2020 21:09:59: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 08 Oct 2020 21:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20_model.r WARNING @ Thu, 08 Oct 2020 21:09:59: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:09:59: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 08 Oct 2020 21:09:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:09:59: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:10:26: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:10:40: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:10:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:10:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:10:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10_summits.bed INFO @ Thu, 08 Oct 2020 21:10:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (15735 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:11:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:11:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:11:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20_summits.bed INFO @ Thu, 08 Oct 2020 21:11:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7822 records, 4 fields): 8 millis CompletedMACS2peakCalling