Job ID = 6627127 SRX = SRX7974998 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: 00:04:27 23176234 reads; of these: 23176234 (100.00%) were unpaired; of these: 5785422 (24.96%) aligned 0 times 14703445 (63.44%) aligned exactly 1 time 2687367 (11.60%) aligned >1 times 75.04% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 2334248 / 17390812 = 0.1342 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 10:16:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.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 10:16:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:16:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:17:01: 1000000 INFO @ Tue, 14 Jul 2020 10:17:09: 2000000 INFO @ Tue, 14 Jul 2020 10:17:18: 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 10:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.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 10:17:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:17:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:17:26: 4000000 INFO @ Tue, 14 Jul 2020 10:17:33: 1000000 INFO @ Tue, 14 Jul 2020 10:17:35: 5000000 INFO @ Tue, 14 Jul 2020 10:17:41: 2000000 INFO @ Tue, 14 Jul 2020 10:17:44: 6000000 INFO @ Tue, 14 Jul 2020 10:17:50: 3000000 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 10:17:52: 7000000 INFO @ Tue, 14 Jul 2020 10:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.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 10:17:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:17:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:17:59: 4000000 INFO @ Tue, 14 Jul 2020 10:18:01: 8000000 INFO @ Tue, 14 Jul 2020 10:18:02: 1000000 INFO @ Tue, 14 Jul 2020 10:18:07: 5000000 INFO @ Tue, 14 Jul 2020 10:18:10: 9000000 INFO @ Tue, 14 Jul 2020 10:18:10: 2000000 INFO @ Tue, 14 Jul 2020 10:18:16: 6000000 INFO @ Tue, 14 Jul 2020 10:18:18: 10000000 INFO @ Tue, 14 Jul 2020 10:18:19: 3000000 INFO @ Tue, 14 Jul 2020 10:18:25: 7000000 INFO @ Tue, 14 Jul 2020 10:18:27: 11000000 INFO @ Tue, 14 Jul 2020 10:18:30: 4000000 INFO @ Tue, 14 Jul 2020 10:18:34: 8000000 INFO @ Tue, 14 Jul 2020 10:18:36: 12000000 INFO @ Tue, 14 Jul 2020 10:18:39: 5000000 INFO @ Tue, 14 Jul 2020 10:18:43: 9000000 INFO @ Tue, 14 Jul 2020 10:18:45: 13000000 INFO @ Tue, 14 Jul 2020 10:18:47: 6000000 INFO @ Tue, 14 Jul 2020 10:18:51: 10000000 INFO @ Tue, 14 Jul 2020 10:18:54: 14000000 INFO @ Tue, 14 Jul 2020 10:18:56: 7000000 INFO @ Tue, 14 Jul 2020 10:19:00: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:19:02: 15000000 INFO @ Tue, 14 Jul 2020 10:19:03: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:19:03: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:19:03: #1 total tags in treatment: 15056564 INFO @ Tue, 14 Jul 2020 10:19:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:19:03: #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 10:19:03: #1 tags after filtering in treatment: 15056558 INFO @ Tue, 14 Jul 2020 10:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:19:03: #1 finished! INFO @ Tue, 14 Jul 2020 10:19:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:19:04: 8000000 INFO @ Tue, 14 Jul 2020 10:19:05: #2 number of paired peaks: 1716 INFO @ Tue, 14 Jul 2020 10:19:05: start model_add_line... INFO @ Tue, 14 Jul 2020 10:19:05: start X-correlation... INFO @ Tue, 14 Jul 2020 10:19:05: end of X-cor INFO @ Tue, 14 Jul 2020 10:19:05: #2 finished! INFO @ Tue, 14 Jul 2020 10:19:05: #2 predicted fragment length is 257 bps INFO @ Tue, 14 Jul 2020 10:19:05: #2 alternative fragment length(s) may be 257 bps INFO @ Tue, 14 Jul 2020 10:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.05_model.r INFO @ Tue, 14 Jul 2020 10:19:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:19:09: 12000000 INFO @ Tue, 14 Jul 2020 10:19:13: 9000000 INFO @ Tue, 14 Jul 2020 10:19:18: 13000000 INFO @ Tue, 14 Jul 2020 10:19:22: 10000000 INFO @ Tue, 14 Jul 2020 10:19:26: 14000000 INFO @ Tue, 14 Jul 2020 10:19:30: 11000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:19:35: 15000000 INFO @ Tue, 14 Jul 2020 10:19:36: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:19:36: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:19:36: #1 total tags in treatment: 15056564 INFO @ Tue, 14 Jul 2020 10:19:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:19:36: #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 10:19:36: #1 tags after filtering in treatment: 15056558 INFO @ Tue, 14 Jul 2020 10:19:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:19:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:19:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:19:37: #2 number of paired peaks: 1716 INFO @ Tue, 14 Jul 2020 10:19:37: start model_add_line... INFO @ Tue, 14 Jul 2020 10:19:37: start X-correlation... INFO @ Tue, 14 Jul 2020 10:19:37: end of X-cor INFO @ Tue, 14 Jul 2020 10:19:37: #2 finished! INFO @ Tue, 14 Jul 2020 10:19:37: #2 predicted fragment length is 257 bps INFO @ Tue, 14 Jul 2020 10:19:37: #2 alternative fragment length(s) may be 257 bps INFO @ Tue, 14 Jul 2020 10:19:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.10_model.r INFO @ Tue, 14 Jul 2020 10:19:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:19:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:19:39: 12000000 INFO @ Tue, 14 Jul 2020 10:19:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:19:47: 13000000 INFO @ Tue, 14 Jul 2020 10:19:55: 14000000 INFO @ Tue, 14 Jul 2020 10:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:20:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.05_summits.bed INFO @ Tue, 14 Jul 2020 10:20:01: Done! pass1 - making usageList (192 chroms): 1 millis pass2 - checking and writing primary data (6703 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:20:02: 15000000 INFO @ Tue, 14 Jul 2020 10:20:03: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 10:20:03: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 10:20:03: #1 total tags in treatment: 15056564 INFO @ Tue, 14 Jul 2020 10:20:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:20:03: #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 10:20:04: #1 tags after filtering in treatment: 15056558 INFO @ Tue, 14 Jul 2020 10:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:20:04: #1 finished! INFO @ Tue, 14 Jul 2020 10:20:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:20:05: #2 number of paired peaks: 1716 INFO @ Tue, 14 Jul 2020 10:20:05: start model_add_line... INFO @ Tue, 14 Jul 2020 10:20:05: start X-correlation... INFO @ Tue, 14 Jul 2020 10:20:05: end of X-cor INFO @ Tue, 14 Jul 2020 10:20:05: #2 finished! INFO @ Tue, 14 Jul 2020 10:20:05: #2 predicted fragment length is 257 bps INFO @ Tue, 14 Jul 2020 10:20:05: #2 alternative fragment length(s) may be 257 bps INFO @ Tue, 14 Jul 2020 10:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.20_model.r INFO @ Tue, 14 Jul 2020 10:20:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:20:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:20:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:20:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:20:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.10_summits.bed INFO @ Tue, 14 Jul 2020 10:20:29: Done! pass1 - making usageList (141 chroms): 1 millis pass2 - checking and writing primary data (5534 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:20:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:20:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:20:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:20:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7974998/SRX7974998.20_summits.bed INFO @ Tue, 14 Jul 2020 10:20:57: Done! pass1 - making usageList (104 chroms): 1 millis pass2 - checking and writing primary data (3921 records, 4 fields): 7 millis CompletedMACS2peakCalling