Job ID = 14167167 SRX = SRX10340465 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 934914 READS because READLEN < 1 Read 10032554 spots for SRR13962474/SRR13962474.sra Written 10032554 spots for SRR13962474/SRR13962474.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167746 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 3 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 1 unmatched pairs [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] 2 unmatched pairs [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] 2 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 3081998 / 6918873 = 0.4454 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted 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 11:13:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.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 11:13:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:13:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:13:46: 1000000 INFO @ Fri, 10 Dec 2021 11:13:53: 2000000 INFO @ Fri, 10 Dec 2021 11:13:59: 3000000 INFO @ Fri, 10 Dec 2021 11:14:06: 4000000 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 11:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.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 11:14:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:14:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:14:13: 5000000 INFO @ Fri, 10 Dec 2021 11:14:17: 1000000 INFO @ Fri, 10 Dec 2021 11:14:20: 6000000 INFO @ Fri, 10 Dec 2021 11:14:24: 2000000 INFO @ Fri, 10 Dec 2021 11:14:27: 7000000 INFO @ Fri, 10 Dec 2021 11:14:31: 3000000 INFO @ Fri, 10 Dec 2021 11:14:35: 8000000 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 11:14:39: 4000000 INFO @ Fri, 10 Dec 2021 11:14:39: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:14:39: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:14:39: #1 total tags in treatment: 3744831 INFO @ Fri, 10 Dec 2021 11:14:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:14:39: #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 11:14:39: #1 tags after filtering in treatment: 3633556 INFO @ Fri, 10 Dec 2021 11:14:39: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:14:39: #1 finished! INFO @ Fri, 10 Dec 2021 11:14:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:14:39: #2 number of paired peaks: 1181 INFO @ Fri, 10 Dec 2021 11:14:39: start model_add_line... INFO @ Fri, 10 Dec 2021 11:14:39: start X-correlation... INFO @ Fri, 10 Dec 2021 11:14:39: end of X-cor INFO @ Fri, 10 Dec 2021 11:14:39: #2 finished! INFO @ Fri, 10 Dec 2021 11:14:39: #2 predicted fragment length is 256 bps INFO @ Fri, 10 Dec 2021 11:14:39: #2 alternative fragment length(s) may be 256 bps INFO @ Fri, 10 Dec 2021 11:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.05_model.r INFO @ Fri, 10 Dec 2021 11:14:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:14:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.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 11:14:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:14:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:14:45: 5000000 INFO @ Fri, 10 Dec 2021 11:14:47: 1000000 INFO @ Fri, 10 Dec 2021 11:14:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:14:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:14:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.05_summits.bed INFO @ Fri, 10 Dec 2021 11:14:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3897 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:14:52: 6000000 INFO @ Fri, 10 Dec 2021 11:14:54: 2000000 INFO @ Fri, 10 Dec 2021 11:14:59: 7000000 INFO @ Fri, 10 Dec 2021 11:15:01: 3000000 INFO @ Fri, 10 Dec 2021 11:15:06: 8000000 INFO @ Fri, 10 Dec 2021 11:15:08: 4000000 INFO @ Fri, 10 Dec 2021 11:15:10: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:15:10: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:15:10: #1 total tags in treatment: 3744831 INFO @ Fri, 10 Dec 2021 11:15:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:15:10: #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 11:15:10: #1 tags after filtering in treatment: 3633556 INFO @ Fri, 10 Dec 2021 11:15:10: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:15:10: #1 finished! INFO @ Fri, 10 Dec 2021 11:15:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:15:10: #2 number of paired peaks: 1181 INFO @ Fri, 10 Dec 2021 11:15:10: start model_add_line... INFO @ Fri, 10 Dec 2021 11:15:10: start X-correlation... INFO @ Fri, 10 Dec 2021 11:15:11: end of X-cor INFO @ Fri, 10 Dec 2021 11:15:11: #2 finished! INFO @ Fri, 10 Dec 2021 11:15:11: #2 predicted fragment length is 256 bps INFO @ Fri, 10 Dec 2021 11:15:11: #2 alternative fragment length(s) may be 256 bps INFO @ Fri, 10 Dec 2021 11:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.10_model.r INFO @ Fri, 10 Dec 2021 11:15:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:15:14: 5000000 INFO @ Fri, 10 Dec 2021 11:15:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:15:21: 6000000 INFO @ Fri, 10 Dec 2021 11:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.10_summits.bed INFO @ Fri, 10 Dec 2021 11:15:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1905 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:15:27: 7000000 INFO @ Fri, 10 Dec 2021 11:15:34: 8000000 INFO @ Fri, 10 Dec 2021 11:15:37: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:15:37: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:15:37: #1 total tags in treatment: 3744831 INFO @ Fri, 10 Dec 2021 11:15:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:15:37: #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 11:15:37: #1 tags after filtering in treatment: 3633556 INFO @ Fri, 10 Dec 2021 11:15:37: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 11:15:37: #1 finished! INFO @ Fri, 10 Dec 2021 11:15:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:15:38: #2 number of paired peaks: 1181 INFO @ Fri, 10 Dec 2021 11:15:38: start model_add_line... INFO @ Fri, 10 Dec 2021 11:15:38: start X-correlation... INFO @ Fri, 10 Dec 2021 11:15:38: end of X-cor INFO @ Fri, 10 Dec 2021 11:15:38: #2 finished! INFO @ Fri, 10 Dec 2021 11:15:38: #2 predicted fragment length is 256 bps INFO @ Fri, 10 Dec 2021 11:15:38: #2 alternative fragment length(s) may be 256 bps INFO @ Fri, 10 Dec 2021 11:15:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.20_model.r INFO @ Fri, 10 Dec 2021 11:15:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:15:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:15:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340465/SRX10340465.20_summits.bed INFO @ Fri, 10 Dec 2021 11:15:50: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (602 records, 4 fields): 39 millis CompletedMACS2peakCalling BigWig に変換しました。