Job ID = 12266654 SRX = SRX7806726 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12114710 spots for SRR11186392/SRR11186392.sra Written 12114710 spots for SRR11186392/SRR11186392.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266936 ("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: 00:18:31 12114710 reads; of these: 12114710 (100.00%) were paired; of these: 6416232 (52.96%) aligned concordantly 0 times 3696824 (30.52%) aligned concordantly exactly 1 time 2001654 (16.52%) aligned concordantly >1 times ---- 6416232 pairs aligned concordantly 0 times; of these: 839031 (13.08%) aligned discordantly 1 time ---- 5577201 pairs aligned 0 times concordantly or discordantly; of these: 11154402 mates make up the pairs; of these: 10007468 (89.72%) aligned 0 times 472030 (4.23%) aligned exactly 1 time 674904 (6.05%) aligned >1 times 58.70% overall alignment rate Time searching: 00:18:31 Overall time: 00:18:31 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1045201 / 6498218 = 0.1608 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.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 @ Sat, 03 Apr 2021 09:27:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:27:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:28:02: 1000000 INFO @ Sat, 03 Apr 2021 09:28:08: 2000000 INFO @ Sat, 03 Apr 2021 09:28:14: 3000000 INFO @ Sat, 03 Apr 2021 09:28:20: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:28:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.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 @ Sat, 03 Apr 2021 09:28:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:28:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:28:26: 5000000 INFO @ Sat, 03 Apr 2021 09:28:34: 6000000 INFO @ Sat, 03 Apr 2021 09:28:34: 1000000 INFO @ Sat, 03 Apr 2021 09:28:41: 7000000 INFO @ Sat, 03 Apr 2021 09:28:42: 2000000 INFO @ Sat, 03 Apr 2021 09:28:49: 8000000 INFO @ Sat, 03 Apr 2021 09:28:49: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.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 @ Sat, 03 Apr 2021 09:28:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:28:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:28:56: 9000000 INFO @ Sat, 03 Apr 2021 09:28:57: 4000000 INFO @ Sat, 03 Apr 2021 09:29:03: 1000000 INFO @ Sat, 03 Apr 2021 09:29:03: 10000000 INFO @ Sat, 03 Apr 2021 09:29:05: 5000000 INFO @ Sat, 03 Apr 2021 09:29:10: 2000000 INFO @ Sat, 03 Apr 2021 09:29:11: 11000000 INFO @ Sat, 03 Apr 2021 09:29:13: 6000000 INFO @ Sat, 03 Apr 2021 09:29:18: 3000000 INFO @ Sat, 03 Apr 2021 09:29:18: 12000000 INFO @ Sat, 03 Apr 2021 09:29:19: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:29:19: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:29:19: #1 total tags in treatment: 4713660 INFO @ Sat, 03 Apr 2021 09:29:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:29:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:29:19: #1 tags after filtering in treatment: 3960042 INFO @ Sat, 03 Apr 2021 09:29:19: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 09:29:19: #1 finished! INFO @ Sat, 03 Apr 2021 09:29:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:29:20: #2 number of paired peaks: 1111 INFO @ Sat, 03 Apr 2021 09:29:20: start model_add_line... INFO @ Sat, 03 Apr 2021 09:29:20: start X-correlation... INFO @ Sat, 03 Apr 2021 09:29:20: end of X-cor INFO @ Sat, 03 Apr 2021 09:29:20: #2 finished! INFO @ Sat, 03 Apr 2021 09:29:20: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Apr 2021 09:29:20: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Apr 2021 09:29:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.05_model.r INFO @ Sat, 03 Apr 2021 09:29:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:29:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:29:21: 7000000 INFO @ Sat, 03 Apr 2021 09:29:26: 4000000 INFO @ Sat, 03 Apr 2021 09:29:29: 8000000 INFO @ Sat, 03 Apr 2021 09:29:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:29:33: 5000000 INFO @ Sat, 03 Apr 2021 09:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.05_summits.bed INFO @ Sat, 03 Apr 2021 09:29:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5291 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:29:36: 9000000 INFO @ Sat, 03 Apr 2021 09:29:41: 6000000 INFO @ Sat, 03 Apr 2021 09:29:44: 10000000 INFO @ Sat, 03 Apr 2021 09:29:48: 7000000 INFO @ Sat, 03 Apr 2021 09:29:52: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:29:56: 8000000 INFO @ Sat, 03 Apr 2021 09:30:00: 12000000 INFO @ Sat, 03 Apr 2021 09:30:01: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:30:01: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:30:01: #1 total tags in treatment: 4713660 INFO @ Sat, 03 Apr 2021 09:30:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:30:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:30:01: #1 tags after filtering in treatment: 3960042 INFO @ Sat, 03 Apr 2021 09:30:01: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 09:30:01: #1 finished! INFO @ Sat, 03 Apr 2021 09:30:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:30:01: #2 number of paired peaks: 1111 INFO @ Sat, 03 Apr 2021 09:30:01: start model_add_line... INFO @ Sat, 03 Apr 2021 09:30:02: start X-correlation... INFO @ Sat, 03 Apr 2021 09:30:02: end of X-cor INFO @ Sat, 03 Apr 2021 09:30:02: #2 finished! INFO @ Sat, 03 Apr 2021 09:30:02: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Apr 2021 09:30:02: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Apr 2021 09:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.10_model.r INFO @ Sat, 03 Apr 2021 09:30:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:30:03: 9000000 INFO @ Sat, 03 Apr 2021 09:30:09: 10000000 INFO @ Sat, 03 Apr 2021 09:30:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:30:15: 11000000 INFO @ Sat, 03 Apr 2021 09:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:30:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.10_summits.bed INFO @ Sat, 03 Apr 2021 09:30:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1974 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:30:22: 12000000 INFO @ Sat, 03 Apr 2021 09:30:23: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:30:23: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:30:23: #1 total tags in treatment: 4713660 INFO @ Sat, 03 Apr 2021 09:30:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:30:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:30:23: #1 tags after filtering in treatment: 3960042 INFO @ Sat, 03 Apr 2021 09:30:23: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 09:30:23: #1 finished! INFO @ Sat, 03 Apr 2021 09:30:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:30:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:30:23: #2 number of paired peaks: 1111 INFO @ Sat, 03 Apr 2021 09:30:23: start model_add_line... INFO @ Sat, 03 Apr 2021 09:30:23: start X-correlation... INFO @ Sat, 03 Apr 2021 09:30:23: end of X-cor INFO @ Sat, 03 Apr 2021 09:30:23: #2 finished! INFO @ Sat, 03 Apr 2021 09:30:23: #2 predicted fragment length is 153 bps INFO @ Sat, 03 Apr 2021 09:30:23: #2 alternative fragment length(s) may be 153 bps INFO @ Sat, 03 Apr 2021 09:30:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.20_model.r INFO @ Sat, 03 Apr 2021 09:30:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:30:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:30:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806726/SRX7806726.20_summits.bed INFO @ Sat, 03 Apr 2021 09:30:38: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 1 millis CompletedMACS2peakCalling