Job ID = 14166977 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 14167331 ("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: 00:17:57 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: 00:17:57 Overall time: 00:17:57 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:45:47: # 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 @ Fri, 10 Dec 2021 08:45:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:45:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:45:52: 1000000 INFO @ Fri, 10 Dec 2021 08:45:58: 2000000 INFO @ Fri, 10 Dec 2021 08:46:03: 3000000 INFO @ Fri, 10 Dec 2021 08:46:09: 4000000 INFO @ Fri, 10 Dec 2021 08:46:14: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:46:17: # 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 @ Fri, 10 Dec 2021 08:46:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:46:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:46:20: 6000000 INFO @ Fri, 10 Dec 2021 08:46:23: 1000000 INFO @ Fri, 10 Dec 2021 08:46:26: 7000000 INFO @ Fri, 10 Dec 2021 08:46:28: 2000000 INFO @ Fri, 10 Dec 2021 08:46:32: 8000000 INFO @ Fri, 10 Dec 2021 08:46:34: 3000000 INFO @ Fri, 10 Dec 2021 08:46:37: 9000000 INFO @ Fri, 10 Dec 2021 08:46:40: 4000000 INFO @ Fri, 10 Dec 2021 08:46:43: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:46:46: 5000000 INFO @ Fri, 10 Dec 2021 08:46:47: # 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 @ Fri, 10 Dec 2021 08:46:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:46:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:46:49: 11000000 INFO @ Fri, 10 Dec 2021 08:46:52: 6000000 INFO @ Fri, 10 Dec 2021 08:46:54: 1000000 INFO @ Fri, 10 Dec 2021 08:46:55: 12000000 INFO @ Fri, 10 Dec 2021 08:46:58: 7000000 INFO @ Fri, 10 Dec 2021 08:47:01: 2000000 INFO @ Fri, 10 Dec 2021 08:47:02: 13000000 INFO @ Fri, 10 Dec 2021 08:47:04: 8000000 INFO @ Fri, 10 Dec 2021 08:47:08: 3000000 INFO @ Fri, 10 Dec 2021 08:47:08: 14000000 INFO @ Fri, 10 Dec 2021 08:47:11: 9000000 INFO @ Fri, 10 Dec 2021 08:47:14: 15000000 INFO @ Fri, 10 Dec 2021 08:47:15: 4000000 INFO @ Fri, 10 Dec 2021 08:47:17: 10000000 INFO @ Fri, 10 Dec 2021 08:47:20: 16000000 INFO @ Fri, 10 Dec 2021 08:47:22: 5000000 INFO @ Fri, 10 Dec 2021 08:47:23: 11000000 INFO @ Fri, 10 Dec 2021 08:47:27: 17000000 INFO @ Fri, 10 Dec 2021 08:47:29: 6000000 INFO @ Fri, 10 Dec 2021 08:47:29: 12000000 INFO @ Fri, 10 Dec 2021 08:47:33: 18000000 INFO @ Fri, 10 Dec 2021 08:47:35: 13000000 INFO @ Fri, 10 Dec 2021 08:47:36: 7000000 INFO @ Fri, 10 Dec 2021 08:47:39: 19000000 INFO @ Fri, 10 Dec 2021 08:47:41: 14000000 INFO @ Fri, 10 Dec 2021 08:47:42: 8000000 INFO @ Fri, 10 Dec 2021 08:47:45: 20000000 INFO @ Fri, 10 Dec 2021 08:47:48: 15000000 INFO @ Fri, 10 Dec 2021 08:47:49: 9000000 INFO @ Fri, 10 Dec 2021 08:47:51: 21000000 INFO @ Fri, 10 Dec 2021 08:47:52: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:47:52: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:47:52: #1 total tags in treatment: 21086171 INFO @ Fri, 10 Dec 2021 08:47:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:47:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:47:52: #1 tags after filtering in treatment: 21086170 INFO @ Fri, 10 Dec 2021 08:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:47:52: #1 finished! INFO @ Fri, 10 Dec 2021 08:47:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:47:54: #2 number of paired peaks: 2770 INFO @ Fri, 10 Dec 2021 08:47:54: start model_add_line... INFO @ Fri, 10 Dec 2021 08:47:54: start X-correlation... INFO @ Fri, 10 Dec 2021 08:47:54: end of X-cor INFO @ Fri, 10 Dec 2021 08:47:54: #2 finished! INFO @ Fri, 10 Dec 2021 08:47:54: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 08:47:54: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 08:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05_model.r INFO @ Fri, 10 Dec 2021 08:47:54: 16000000 WARNING @ Fri, 10 Dec 2021 08:47:54: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:47:54: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 08:47:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:47:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:47:56: 10000000 INFO @ Fri, 10 Dec 2021 08:48:00: 17000000 INFO @ Fri, 10 Dec 2021 08:48:03: 11000000 INFO @ Fri, 10 Dec 2021 08:48:06: 18000000 INFO @ Fri, 10 Dec 2021 08:48:10: 12000000 INFO @ Fri, 10 Dec 2021 08:48:12: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:48:17: 13000000 INFO @ Fri, 10 Dec 2021 08:48:18: 20000000 INFO @ Fri, 10 Dec 2021 08:48:24: 14000000 INFO @ Fri, 10 Dec 2021 08:48:25: 21000000 INFO @ Fri, 10 Dec 2021 08:48:25: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:48:25: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:48:25: #1 total tags in treatment: 21086171 INFO @ Fri, 10 Dec 2021 08:48:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:48:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:48:25: #1 tags after filtering in treatment: 21086170 INFO @ Fri, 10 Dec 2021 08:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:48:25: #1 finished! INFO @ Fri, 10 Dec 2021 08:48:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:48:27: #2 number of paired peaks: 2770 INFO @ Fri, 10 Dec 2021 08:48:27: start model_add_line... INFO @ Fri, 10 Dec 2021 08:48:27: start X-correlation... INFO @ Fri, 10 Dec 2021 08:48:27: end of X-cor INFO @ Fri, 10 Dec 2021 08:48:27: #2 finished! INFO @ Fri, 10 Dec 2021 08:48:27: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 08:48:27: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 08:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10_model.r WARNING @ Fri, 10 Dec 2021 08:48:27: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:48:27: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 08:48:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:48:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:48:30: 15000000 INFO @ Fri, 10 Dec 2021 08:48:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:48:37: 16000000 INFO @ Fri, 10 Dec 2021 08:48:43: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:48:50: 18000000 INFO @ Fri, 10 Dec 2021 08:48:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:48:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:48:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.05_summits.bed INFO @ Fri, 10 Dec 2021 08:48:53: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (25349 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:48:56: 19000000 INFO @ Fri, 10 Dec 2021 08:49:03: 20000000 INFO @ Fri, 10 Dec 2021 08:49:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:49:09: 21000000 INFO @ Fri, 10 Dec 2021 08:49:10: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:49:10: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:49:10: #1 total tags in treatment: 21086171 INFO @ Fri, 10 Dec 2021 08:49:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:49:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:49:10: #1 tags after filtering in treatment: 21086170 INFO @ Fri, 10 Dec 2021 08:49:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:49:10: #1 finished! INFO @ Fri, 10 Dec 2021 08:49:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:49:12: #2 number of paired peaks: 2770 INFO @ Fri, 10 Dec 2021 08:49:12: start model_add_line... INFO @ Fri, 10 Dec 2021 08:49:12: start X-correlation... INFO @ Fri, 10 Dec 2021 08:49:12: end of X-cor INFO @ Fri, 10 Dec 2021 08:49:12: #2 finished! INFO @ Fri, 10 Dec 2021 08:49:12: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 08:49:12: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 08:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20_model.r WARNING @ Fri, 10 Dec 2021 08:49:12: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:49:12: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 08:49:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:49:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:49:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:49:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:49:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.10_summits.bed INFO @ Fri, 10 Dec 2021 08:49:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (15735 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:49:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723710/SRX7723710.20_summits.bed INFO @ Fri, 10 Dec 2021 08:50:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7822 records, 4 fields): 8 millis CompletedMACS2peakCalling