Job ID = 6626982 SRX = SRX7974998 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23176234 spots for SRR11396281/SRR11396281.sra Written 23176234 spots for SRR11396281/SRR11396281.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627127 ("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: 00:05:50 23176234 reads; of these: 23176234 (100.00%) were unpaired; of these: 5690369 (24.55%) aligned 0 times 14682684 (63.35%) aligned exactly 1 time 2803181 (12.10%) aligned >1 times 75.45% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 2189213 / 17485865 = 0.1252 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 09:21:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 09:21:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:21:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:21:57: 1000000 INFO @ Tue, 14 Jul 2020 09:22:03: 2000000 INFO @ Tue, 14 Jul 2020 09:22:09: 3000000 INFO @ Tue, 14 Jul 2020 09:22:15: 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 @ Tue, 14 Jul 2020 09:22:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 09:22:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:22:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:22:21: 5000000 INFO @ Tue, 14 Jul 2020 09:22:27: 1000000 INFO @ Tue, 14 Jul 2020 09:22:27: 6000000 INFO @ Tue, 14 Jul 2020 09:22:33: 7000000 INFO @ Tue, 14 Jul 2020 09:22:33: 2000000 INFO @ Tue, 14 Jul 2020 09:22:40: 8000000 INFO @ Tue, 14 Jul 2020 09:22:40: 3000000 INFO @ Tue, 14 Jul 2020 09:22:46: 9000000 INFO @ Tue, 14 Jul 2020 09:22:46: 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 09:22:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 09:22:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:22:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:22:52: 10000000 INFO @ Tue, 14 Jul 2020 09:22:52: 5000000 INFO @ Tue, 14 Jul 2020 09:22:58: 1000000 INFO @ Tue, 14 Jul 2020 09:22:59: 11000000 INFO @ Tue, 14 Jul 2020 09:22:59: 6000000 INFO @ Tue, 14 Jul 2020 09:23:05: 12000000 INFO @ Tue, 14 Jul 2020 09:23:05: 2000000 INFO @ Tue, 14 Jul 2020 09:23:06: 7000000 INFO @ Tue, 14 Jul 2020 09:23:12: 13000000 INFO @ Tue, 14 Jul 2020 09:23:12: 8000000 INFO @ Tue, 14 Jul 2020 09:23:13: 3000000 INFO @ Tue, 14 Jul 2020 09:23:19: 9000000 INFO @ Tue, 14 Jul 2020 09:23:19: 14000000 INFO @ Tue, 14 Jul 2020 09:23:19: 4000000 INFO @ Tue, 14 Jul 2020 09:23:25: 10000000 INFO @ Tue, 14 Jul 2020 09:23:25: 15000000 INFO @ Tue, 14 Jul 2020 09:23:26: 5000000 INFO @ Tue, 14 Jul 2020 09:23:27: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:23:27: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:23:27: #1 total tags in treatment: 15296652 INFO @ Tue, 14 Jul 2020 09:23:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:23:27: #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 09:23:28: #1 tags after filtering in treatment: 15296652 INFO @ Tue, 14 Jul 2020 09:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:23:28: #1 finished! INFO @ Tue, 14 Jul 2020 09:23:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:23:29: #2 number of paired peaks: 1479 INFO @ Tue, 14 Jul 2020 09:23:29: start model_add_line... INFO @ Tue, 14 Jul 2020 09:23:29: start X-correlation... INFO @ Tue, 14 Jul 2020 09:23:29: end of X-cor INFO @ Tue, 14 Jul 2020 09:23:29: #2 finished! INFO @ Tue, 14 Jul 2020 09:23:29: #2 predicted fragment length is 251 bps INFO @ Tue, 14 Jul 2020 09:23:29: #2 alternative fragment length(s) may be 251 bps INFO @ Tue, 14 Jul 2020 09:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.05_model.r INFO @ Tue, 14 Jul 2020 09:23:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:23:32: 11000000 INFO @ Tue, 14 Jul 2020 09:23:33: 6000000 INFO @ Tue, 14 Jul 2020 09:23:38: 12000000 INFO @ Tue, 14 Jul 2020 09:23:40: 7000000 INFO @ Tue, 14 Jul 2020 09:23:45: 13000000 INFO @ Tue, 14 Jul 2020 09:23:47: 8000000 INFO @ Tue, 14 Jul 2020 09:23:51: 14000000 INFO @ Tue, 14 Jul 2020 09:23:54: 9000000 INFO @ Tue, 14 Jul 2020 09:23:58: 15000000 INFO @ Tue, 14 Jul 2020 09:24:00: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:24:00: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:24:00: #1 total tags in treatment: 15296652 INFO @ Tue, 14 Jul 2020 09:24:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:24:00: #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 09:24:00: #1 tags after filtering in treatment: 15296652 INFO @ Tue, 14 Jul 2020 09:24:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:24:00: #1 finished! INFO @ Tue, 14 Jul 2020 09:24:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:24:01: 10000000 INFO @ Tue, 14 Jul 2020 09:24:02: #2 number of paired peaks: 1479 INFO @ Tue, 14 Jul 2020 09:24:02: start model_add_line... INFO @ Tue, 14 Jul 2020 09:24:02: start X-correlation... INFO @ Tue, 14 Jul 2020 09:24:02: end of X-cor INFO @ Tue, 14 Jul 2020 09:24:02: #2 finished! INFO @ Tue, 14 Jul 2020 09:24:02: #2 predicted fragment length is 251 bps INFO @ Tue, 14 Jul 2020 09:24:02: #2 alternative fragment length(s) may be 251 bps INFO @ Tue, 14 Jul 2020 09:24:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.10_model.r INFO @ Tue, 14 Jul 2020 09:24:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:24:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:24:08: 11000000 INFO @ Tue, 14 Jul 2020 09:24:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:24:15: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:24:21: 13000000 INFO @ Tue, 14 Jul 2020 09:24:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:24:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:24:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.05_summits.bed INFO @ Tue, 14 Jul 2020 09:24:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6802 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:24:28: 14000000 INFO @ Tue, 14 Jul 2020 09:24:35: 15000000 INFO @ Tue, 14 Jul 2020 09:24:37: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:24:37: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:24:37: #1 total tags in treatment: 15296652 INFO @ Tue, 14 Jul 2020 09:24:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:24:37: #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 09:24:38: #1 tags after filtering in treatment: 15296652 INFO @ Tue, 14 Jul 2020 09:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:24:38: #1 finished! INFO @ Tue, 14 Jul 2020 09:24:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:24:39: #2 number of paired peaks: 1479 INFO @ Tue, 14 Jul 2020 09:24:39: start model_add_line... INFO @ Tue, 14 Jul 2020 09:24:39: start X-correlation... INFO @ Tue, 14 Jul 2020 09:24:39: end of X-cor INFO @ Tue, 14 Jul 2020 09:24:39: #2 finished! INFO @ Tue, 14 Jul 2020 09:24:39: #2 predicted fragment length is 251 bps INFO @ Tue, 14 Jul 2020 09:24:39: #2 alternative fragment length(s) may be 251 bps INFO @ Tue, 14 Jul 2020 09:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.20_model.r INFO @ Tue, 14 Jul 2020 09:24:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:24:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:24:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.10_summits.bed INFO @ Tue, 14 Jul 2020 09:25:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5676 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:25:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974998/SRX7974998.20_summits.bed INFO @ Tue, 14 Jul 2020 09:25:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4020 records, 4 fields): 6 millis CompletedMACS2peakCalling