Job ID = 12266655 SRX = SRX7806727 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14583932 spots for SRR11186393/SRR11186393.sra Written 14583932 spots for SRR11186393/SRR11186393.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266989 ("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: 00:23:33 14583932 reads; of these: 14583932 (100.00%) were paired; of these: 7620192 (52.25%) aligned concordantly 0 times 4496678 (30.83%) aligned concordantly exactly 1 time 2467062 (16.92%) aligned concordantly >1 times ---- 7620192 pairs aligned concordantly 0 times; of these: 1087357 (14.27%) aligned discordantly 1 time ---- 6532835 pairs aligned 0 times concordantly or discordantly; of these: 13065670 mates make up the pairs; of these: 11603153 (88.81%) aligned 0 times 617031 (4.72%) aligned exactly 1 time 845486 (6.47%) aligned >1 times 60.22% overall alignment rate Time searching: 00:23:33 Overall time: 00:23:33 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] 1484888 / 8001840 = 0.1856 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 09:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.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 09:34:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:34:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:34:28: 1000000 INFO @ Sat, 03 Apr 2021 09:34:34: 2000000 INFO @ Sat, 03 Apr 2021 09:34:40: 3000000 INFO @ Sat, 03 Apr 2021 09:34:46: 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 09:34:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.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 09:34:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:34:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:34:53: 5000000 INFO @ Sat, 03 Apr 2021 09:34:59: 1000000 INFO @ Sat, 03 Apr 2021 09:35:00: 6000000 INFO @ Sat, 03 Apr 2021 09:35:07: 7000000 INFO @ Sat, 03 Apr 2021 09:35:08: 2000000 INFO @ Sat, 03 Apr 2021 09:35:15: 8000000 INFO @ Sat, 03 Apr 2021 09:35:16: 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 09:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.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 09:35:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:35:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:35:22: 9000000 INFO @ Sat, 03 Apr 2021 09:35:24: 4000000 INFO @ Sat, 03 Apr 2021 09:35:29: 1000000 INFO @ Sat, 03 Apr 2021 09:35:29: 10000000 INFO @ Sat, 03 Apr 2021 09:35:32: 5000000 INFO @ Sat, 03 Apr 2021 09:35:37: 11000000 INFO @ Sat, 03 Apr 2021 09:35:37: 2000000 INFO @ Sat, 03 Apr 2021 09:35:40: 6000000 INFO @ Sat, 03 Apr 2021 09:35:44: 12000000 INFO @ Sat, 03 Apr 2021 09:35:44: 3000000 INFO @ Sat, 03 Apr 2021 09:35:48: 7000000 INFO @ Sat, 03 Apr 2021 09:35:52: 13000000 INFO @ Sat, 03 Apr 2021 09:35:52: 4000000 INFO @ Sat, 03 Apr 2021 09:35:56: 8000000 INFO @ Sat, 03 Apr 2021 09:35:59: 14000000 INFO @ Sat, 03 Apr 2021 09:35:59: 5000000 INFO @ Sat, 03 Apr 2021 09:36:04: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:36:04: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:36:04: #1 total tags in treatment: 5568470 INFO @ Sat, 03 Apr 2021 09:36:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:36:04: #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 09:36:04: #1 tags after filtering in treatment: 4589316 INFO @ Sat, 03 Apr 2021 09:36:04: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 09:36:04: #1 finished! INFO @ Sat, 03 Apr 2021 09:36:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:36:04: #2 number of paired peaks: 1570 INFO @ Sat, 03 Apr 2021 09:36:04: 9000000 INFO @ Sat, 03 Apr 2021 09:36:04: start model_add_line... INFO @ Sat, 03 Apr 2021 09:36:04: start X-correlation... INFO @ Sat, 03 Apr 2021 09:36:04: end of X-cor INFO @ Sat, 03 Apr 2021 09:36:04: #2 finished! INFO @ Sat, 03 Apr 2021 09:36:04: #2 predicted fragment length is 156 bps INFO @ Sat, 03 Apr 2021 09:36:04: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 03 Apr 2021 09:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.05_model.r INFO @ Sat, 03 Apr 2021 09:36:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:36:07: 6000000 INFO @ Sat, 03 Apr 2021 09:36:12: 10000000 INFO @ Sat, 03 Apr 2021 09:36:15: 7000000 INFO @ Sat, 03 Apr 2021 09:36:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:36:20: 11000000 INFO @ Sat, 03 Apr 2021 09:36:22: 8000000 INFO @ Sat, 03 Apr 2021 09:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.05_summits.bed INFO @ Sat, 03 Apr 2021 09:36:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7301 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:36:28: 12000000 INFO @ Sat, 03 Apr 2021 09:36:30: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:36:36: 13000000 INFO @ Sat, 03 Apr 2021 09:36:37: 10000000 INFO @ Sat, 03 Apr 2021 09:36:44: 14000000 INFO @ Sat, 03 Apr 2021 09:36:44: 11000000 INFO @ Sat, 03 Apr 2021 09:36:49: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:36:49: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:36:49: #1 total tags in treatment: 5568470 INFO @ Sat, 03 Apr 2021 09:36:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:36:49: #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 09:36:49: #1 tags after filtering in treatment: 4589316 INFO @ Sat, 03 Apr 2021 09:36:49: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 09:36:49: #1 finished! INFO @ Sat, 03 Apr 2021 09:36:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:36:49: #2 number of paired peaks: 1570 INFO @ Sat, 03 Apr 2021 09:36:49: start model_add_line... INFO @ Sat, 03 Apr 2021 09:36:49: start X-correlation... INFO @ Sat, 03 Apr 2021 09:36:49: end of X-cor INFO @ Sat, 03 Apr 2021 09:36:49: #2 finished! INFO @ Sat, 03 Apr 2021 09:36:49: #2 predicted fragment length is 156 bps INFO @ Sat, 03 Apr 2021 09:36:49: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 03 Apr 2021 09:36:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.10_model.r INFO @ Sat, 03 Apr 2021 09:36:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:36:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:36:51: 12000000 INFO @ Sat, 03 Apr 2021 09:36:57: 13000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:37:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:37:03: 14000000 INFO @ Sat, 03 Apr 2021 09:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.10_summits.bed INFO @ Sat, 03 Apr 2021 09:37:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3101 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:37:07: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:37:07: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:37:07: #1 total tags in treatment: 5568470 INFO @ Sat, 03 Apr 2021 09:37:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:37:07: #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 09:37:07: #1 tags after filtering in treatment: 4589316 INFO @ Sat, 03 Apr 2021 09:37:07: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 09:37:07: #1 finished! INFO @ Sat, 03 Apr 2021 09:37:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:37:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:37:07: #2 number of paired peaks: 1570 INFO @ Sat, 03 Apr 2021 09:37:07: start model_add_line... INFO @ Sat, 03 Apr 2021 09:37:07: start X-correlation... INFO @ Sat, 03 Apr 2021 09:37:07: end of X-cor INFO @ Sat, 03 Apr 2021 09:37:07: #2 finished! INFO @ Sat, 03 Apr 2021 09:37:07: #2 predicted fragment length is 156 bps INFO @ Sat, 03 Apr 2021 09:37:07: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 03 Apr 2021 09:37:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.20_model.r INFO @ Sat, 03 Apr 2021 09:37:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:37:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:37:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806727/SRX7806727.20_summits.bed INFO @ Sat, 03 Apr 2021 09:37:24: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (777 records, 4 fields): 3 millis CompletedMACS2peakCalling