Job ID = 14170555 SRX = SRX9372356 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16093899 spots for SRR12907633/SRR12907633.sra Written 16093899 spots for SRR12907633/SRR12907633.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170988 ("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: 00:11:22 16093899 reads; of these: 16093899 (100.00%) were paired; of these: 8653236 (53.77%) aligned concordantly 0 times 6445910 (40.05%) aligned concordantly exactly 1 time 994753 (6.18%) aligned concordantly >1 times ---- 8653236 pairs aligned concordantly 0 times; of these: 1126702 (13.02%) aligned discordantly 1 time ---- 7526534 pairs aligned 0 times concordantly or discordantly; of these: 15053068 mates make up the pairs; of these: 14028802 (93.20%) aligned 0 times 682016 (4.53%) aligned exactly 1 time 342250 (2.27%) aligned >1 times 56.42% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 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] 1624830 / 8550956 = 0.1900 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 @ Sat, 11 Dec 2021 07:27:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.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, 11 Dec 2021 07:27:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:27:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:27:59: 1000000 INFO @ Sat, 11 Dec 2021 07:28:04: 2000000 INFO @ Sat, 11 Dec 2021 07:28:09: 3000000 INFO @ Sat, 11 Dec 2021 07:28:14: 4000000 INFO @ Sat, 11 Dec 2021 07:28:19: 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 @ Sat, 11 Dec 2021 07:28:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.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, 11 Dec 2021 07:28:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:28:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:28:24: 6000000 INFO @ Sat, 11 Dec 2021 07:28:29: 1000000 INFO @ Sat, 11 Dec 2021 07:28:29: 7000000 INFO @ Sat, 11 Dec 2021 07:28:34: 8000000 INFO @ Sat, 11 Dec 2021 07:28:34: 2000000 INFO @ Sat, 11 Dec 2021 07:28:39: 9000000 INFO @ Sat, 11 Dec 2021 07:28:39: 3000000 INFO @ Sat, 11 Dec 2021 07:28:45: 10000000 INFO @ Sat, 11 Dec 2021 07:28:45: 4000000 INFO @ Sat, 11 Dec 2021 07:28:50: 11000000 INFO @ Sat, 11 Dec 2021 07:28:50: 5000000 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 @ Sat, 11 Dec 2021 07:28:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.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, 11 Dec 2021 07:28:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:28:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:28:55: 12000000 INFO @ Sat, 11 Dec 2021 07:28:55: 6000000 INFO @ Sat, 11 Dec 2021 07:28:58: 1000000 INFO @ Sat, 11 Dec 2021 07:29:00: 7000000 INFO @ Sat, 11 Dec 2021 07:29:00: 13000000 INFO @ Sat, 11 Dec 2021 07:29:02: 2000000 INFO @ Sat, 11 Dec 2021 07:29:06: 8000000 INFO @ Sat, 11 Dec 2021 07:29:06: 14000000 INFO @ Sat, 11 Dec 2021 07:29:07: 3000000 INFO @ Sat, 11 Dec 2021 07:29:11: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:29:11: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:29:11: #1 total tags in treatment: 5978254 INFO @ Sat, 11 Dec 2021 07:29:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:29:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:29:11: #1 tags after filtering in treatment: 5734489 INFO @ Sat, 11 Dec 2021 07:29:11: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 07:29:11: #1 finished! INFO @ Sat, 11 Dec 2021 07:29:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:29:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:29:11: 9000000 INFO @ Sat, 11 Dec 2021 07:29:11: 4000000 INFO @ Sat, 11 Dec 2021 07:29:11: #2 number of paired peaks: 5419 INFO @ Sat, 11 Dec 2021 07:29:11: start model_add_line... INFO @ Sat, 11 Dec 2021 07:29:11: start X-correlation... INFO @ Sat, 11 Dec 2021 07:29:11: end of X-cor INFO @ Sat, 11 Dec 2021 07:29:11: #2 finished! INFO @ Sat, 11 Dec 2021 07:29:11: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 07:29:11: #2 alternative fragment length(s) may be 4,269 bps INFO @ Sat, 11 Dec 2021 07:29:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.05_model.r INFO @ Sat, 11 Dec 2021 07:29:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:29:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:29:16: 5000000 INFO @ Sat, 11 Dec 2021 07:29:16: 10000000 INFO @ Sat, 11 Dec 2021 07:29:20: 6000000 INFO @ Sat, 11 Dec 2021 07:29:21: 11000000 INFO @ Sat, 11 Dec 2021 07:29:24: 7000000 INFO @ Sat, 11 Dec 2021 07:29:26: 12000000 INFO @ Sat, 11 Dec 2021 07:29:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:29:29: 8000000 INFO @ Sat, 11 Dec 2021 07:29:32: 13000000 INFO @ Sat, 11 Dec 2021 07:29:33: 9000000 INFO @ Sat, 11 Dec 2021 07:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.05_summits.bed INFO @ Sat, 11 Dec 2021 07:29:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (718 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:29:37: 14000000 INFO @ Sat, 11 Dec 2021 07:29:37: 10000000 INFO @ Sat, 11 Dec 2021 07:29:42: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:29:42: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:29:42: #1 total tags in treatment: 5978254 INFO @ Sat, 11 Dec 2021 07:29:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:29:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:29:42: 11000000 INFO @ Sat, 11 Dec 2021 07:29:42: #1 tags after filtering in treatment: 5734489 INFO @ Sat, 11 Dec 2021 07:29:42: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 07:29:42: #1 finished! INFO @ Sat, 11 Dec 2021 07:29:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:29:42: #2 number of paired peaks: 5419 INFO @ Sat, 11 Dec 2021 07:29:42: start model_add_line... INFO @ Sat, 11 Dec 2021 07:29:42: start X-correlation... INFO @ Sat, 11 Dec 2021 07:29:42: end of X-cor INFO @ Sat, 11 Dec 2021 07:29:42: #2 finished! INFO @ Sat, 11 Dec 2021 07:29:42: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 07:29:42: #2 alternative fragment length(s) may be 4,269 bps INFO @ Sat, 11 Dec 2021 07:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.10_model.r INFO @ Sat, 11 Dec 2021 07:29:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:29:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:29:46: 12000000 INFO @ Sat, 11 Dec 2021 07:29:50: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:29:54: 14000000 INFO @ Sat, 11 Dec 2021 07:29:58: #1 tag size is determined as 43 bps INFO @ Sat, 11 Dec 2021 07:29:58: #1 tag size = 43 INFO @ Sat, 11 Dec 2021 07:29:58: #1 total tags in treatment: 5978254 INFO @ Sat, 11 Dec 2021 07:29:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:29:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:29:58: #1 tags after filtering in treatment: 5734489 INFO @ Sat, 11 Dec 2021 07:29:58: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 07:29:58: #1 finished! INFO @ Sat, 11 Dec 2021 07:29:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:29:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:29:59: #2 number of paired peaks: 5419 INFO @ Sat, 11 Dec 2021 07:29:59: start model_add_line... INFO @ Sat, 11 Dec 2021 07:29:59: start X-correlation... INFO @ Sat, 11 Dec 2021 07:29:59: end of X-cor INFO @ Sat, 11 Dec 2021 07:29:59: #2 finished! INFO @ Sat, 11 Dec 2021 07:29:59: #2 predicted fragment length is 269 bps INFO @ Sat, 11 Dec 2021 07:29:59: #2 alternative fragment length(s) may be 4,269 bps INFO @ Sat, 11 Dec 2021 07:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.20_model.r INFO @ Sat, 11 Dec 2021 07:29:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.10_summits.bed INFO @ Sat, 11 Dec 2021 07:30:06: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (254 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:30:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:30:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9372356/SRX9372356.20_summits.bed INFO @ Sat, 11 Dec 2021 07:30:19: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (92 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。