Job ID = 14167973 SRX = ERX3978924 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 37553438 spots for ERR3975993/ERR3975993.sra Written 37553438 spots for ERR3975993/ERR3975993.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168930 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:37:08 37553438 reads; of these: 37553438 (100.00%) were paired; of these: 4533363 (12.07%) aligned concordantly 0 times 26362075 (70.20%) aligned concordantly exactly 1 time 6658000 (17.73%) aligned concordantly >1 times ---- 4533363 pairs aligned concordantly 0 times; of these: 814621 (17.97%) aligned discordantly 1 time ---- 3718742 pairs aligned 0 times concordantly or discordantly; of these: 7437484 mates make up the pairs; of these: 3914769 (52.64%) aligned 0 times 1613863 (21.70%) aligned exactly 1 time 1908852 (25.67%) aligned >1 times 94.79% overall alignment rate Time searching: 01:37:12 Overall time: 01:37:12 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 32 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] 27314715 / 33697903 = 0.8106 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 15:54:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.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 15:54:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:54:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:54:45: 1000000 INFO @ Fri, 10 Dec 2021 15:54:50: 2000000 INFO @ Fri, 10 Dec 2021 15:54:56: 3000000 INFO @ Fri, 10 Dec 2021 15:55:02: 4000000 INFO @ Fri, 10 Dec 2021 15:55:07: 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 15:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.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 15:55:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:55:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:55:13: 6000000 INFO @ Fri, 10 Dec 2021 15:55:16: 1000000 INFO @ Fri, 10 Dec 2021 15:55:20: 7000000 INFO @ Fri, 10 Dec 2021 15:55:22: 2000000 INFO @ Fri, 10 Dec 2021 15:55:26: 8000000 INFO @ Fri, 10 Dec 2021 15:55:29: 3000000 INFO @ Fri, 10 Dec 2021 15:55:33: 9000000 INFO @ Fri, 10 Dec 2021 15:55:35: 4000000 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 15:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.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 15:55:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:55:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:55:40: 10000000 INFO @ Fri, 10 Dec 2021 15:55:42: 5000000 INFO @ Fri, 10 Dec 2021 15:55:47: 11000000 INFO @ Fri, 10 Dec 2021 15:55:47: 1000000 INFO @ Fri, 10 Dec 2021 15:55:49: 6000000 INFO @ Fri, 10 Dec 2021 15:55:54: 12000000 INFO @ Fri, 10 Dec 2021 15:55:56: 2000000 INFO @ Fri, 10 Dec 2021 15:55:56: 7000000 INFO @ Fri, 10 Dec 2021 15:56:01: 13000000 INFO @ Fri, 10 Dec 2021 15:56:03: 8000000 INFO @ Fri, 10 Dec 2021 15:56:04: 3000000 INFO @ Fri, 10 Dec 2021 15:56:09: 14000000 INFO @ Fri, 10 Dec 2021 15:56:11: 9000000 INFO @ Fri, 10 Dec 2021 15:56:12: 4000000 INFO @ Fri, 10 Dec 2021 15:56:16: 15000000 INFO @ Fri, 10 Dec 2021 15:56:18: 10000000 INFO @ Fri, 10 Dec 2021 15:56:20: 5000000 INFO @ Fri, 10 Dec 2021 15:56:23: 16000000 INFO @ Fri, 10 Dec 2021 15:56:25: 11000000 INFO @ Fri, 10 Dec 2021 15:56:27: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:56:27: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:56:27: #1 total tags in treatment: 6349318 INFO @ Fri, 10 Dec 2021 15:56:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:56:27: #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 15:56:27: #1 tags after filtering in treatment: 5621383 INFO @ Fri, 10 Dec 2021 15:56:27: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 15:56:27: #1 finished! INFO @ Fri, 10 Dec 2021 15:56:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:56:27: #2 number of paired peaks: 4746 INFO @ Fri, 10 Dec 2021 15:56:27: start model_add_line... INFO @ Fri, 10 Dec 2021 15:56:28: start X-correlation... INFO @ Fri, 10 Dec 2021 15:56:28: end of X-cor INFO @ Fri, 10 Dec 2021 15:56:28: #2 finished! INFO @ Fri, 10 Dec 2021 15:56:28: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 15:56:28: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 15:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.05_model.r INFO @ Fri, 10 Dec 2021 15:56:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:56:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:56:28: 6000000 INFO @ Fri, 10 Dec 2021 15:56:32: 12000000 INFO @ Fri, 10 Dec 2021 15:56:36: 7000000 INFO @ Fri, 10 Dec 2021 15:56:39: 13000000 INFO @ Fri, 10 Dec 2021 15:56:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:56:44: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:56:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:56:46: 14000000 INFO @ Fri, 10 Dec 2021 15:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.05_summits.bed INFO @ Fri, 10 Dec 2021 15:56:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11599 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:56:53: 9000000 INFO @ Fri, 10 Dec 2021 15:56:54: 15000000 INFO @ Fri, 10 Dec 2021 15:57:01: 16000000 INFO @ Fri, 10 Dec 2021 15:57:01: 10000000 INFO @ Fri, 10 Dec 2021 15:57:04: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:57:04: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:57:04: #1 total tags in treatment: 6349318 INFO @ Fri, 10 Dec 2021 15:57:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:57:04: #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 15:57:04: #1 tags after filtering in treatment: 5621383 INFO @ Fri, 10 Dec 2021 15:57:04: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 15:57:04: #1 finished! INFO @ Fri, 10 Dec 2021 15:57:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:57:05: #2 number of paired peaks: 4746 INFO @ Fri, 10 Dec 2021 15:57:05: start model_add_line... INFO @ Fri, 10 Dec 2021 15:57:05: start X-correlation... INFO @ Fri, 10 Dec 2021 15:57:05: end of X-cor INFO @ Fri, 10 Dec 2021 15:57:05: #2 finished! INFO @ Fri, 10 Dec 2021 15:57:05: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 15:57:05: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 15:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.10_model.r INFO @ Fri, 10 Dec 2021 15:57:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:57:09: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:57:17: 12000000 INFO @ Fri, 10 Dec 2021 15:57:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:57:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.10_summits.bed INFO @ Fri, 10 Dec 2021 15:57:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8069 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:57:24: 13000000 INFO @ Fri, 10 Dec 2021 15:57:32: 14000000 INFO @ Fri, 10 Dec 2021 15:57:39: 15000000 INFO @ Fri, 10 Dec 2021 15:57:47: 16000000 INFO @ Fri, 10 Dec 2021 15:57:51: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:57:51: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:57:51: #1 total tags in treatment: 6349318 INFO @ Fri, 10 Dec 2021 15:57:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:57:51: #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 15:57:51: #1 tags after filtering in treatment: 5621383 INFO @ Fri, 10 Dec 2021 15:57:51: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 15:57:51: #1 finished! INFO @ Fri, 10 Dec 2021 15:57:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:57:51: #2 number of paired peaks: 4746 INFO @ Fri, 10 Dec 2021 15:57:51: start model_add_line... INFO @ Fri, 10 Dec 2021 15:57:51: start X-correlation... INFO @ Fri, 10 Dec 2021 15:57:51: end of X-cor INFO @ Fri, 10 Dec 2021 15:57:51: #2 finished! INFO @ Fri, 10 Dec 2021 15:57:51: #2 predicted fragment length is 179 bps INFO @ Fri, 10 Dec 2021 15:57:51: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 10 Dec 2021 15:57:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.20_model.r INFO @ Fri, 10 Dec 2021 15:57:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:57:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:58:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978924/ERX3978924.20_summits.bed INFO @ Fri, 10 Dec 2021 15:58:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4614 records, 4 fields): 6 millis CompletedMACS2peakCalling