Job ID = 14167162 SRX = SRX10340460 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1241099 READS because READLEN < 1 Read 11564847 spots for SRR13962469/SRR13962469.sra Written 11564847 spots for SRR13962469/SRR13962469.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167719 ("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] 3 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] 1 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2429460 / 8872845 = 0.2738 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 11:03:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.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 11:03:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:03:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:03:25: 1000000 INFO @ Fri, 10 Dec 2021 11:03:31: 2000000 INFO @ Fri, 10 Dec 2021 11:03:37: 3000000 INFO @ Fri, 10 Dec 2021 11:03:43: 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 11:03:49: 5000000 INFO @ Fri, 10 Dec 2021 11:03:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.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 11:03:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:03:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:03:56: 6000000 INFO @ Fri, 10 Dec 2021 11:03:56: 1000000 INFO @ Fri, 10 Dec 2021 11:04:02: 7000000 INFO @ Fri, 10 Dec 2021 11:04:03: 2000000 INFO @ Fri, 10 Dec 2021 11:04:08: 8000000 INFO @ Fri, 10 Dec 2021 11:04:09: 3000000 INFO @ Fri, 10 Dec 2021 11:04:14: 9000000 INFO @ Fri, 10 Dec 2021 11:04:16: 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 11:04:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.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 11:04:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:04:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:04:20: 10000000 INFO @ Fri, 10 Dec 2021 11:04:22: 5000000 INFO @ Fri, 10 Dec 2021 11:04:26: 1000000 INFO @ Fri, 10 Dec 2021 11:04:26: 11000000 INFO @ Fri, 10 Dec 2021 11:04:28: 6000000 INFO @ Fri, 10 Dec 2021 11:04:31: 2000000 INFO @ Fri, 10 Dec 2021 11:04:32: 12000000 INFO @ Fri, 10 Dec 2021 11:04:34: 7000000 INFO @ Fri, 10 Dec 2021 11:04:37: 3000000 INFO @ Fri, 10 Dec 2021 11:04:38: 13000000 INFO @ Fri, 10 Dec 2021 11:04:40: 8000000 INFO @ Fri, 10 Dec 2021 11:04:44: 4000000 INFO @ Fri, 10 Dec 2021 11:04:45: 14000000 INFO @ Fri, 10 Dec 2021 11:04:45: #1 tag size is determined as 121 bps INFO @ Fri, 10 Dec 2021 11:04:45: #1 tag size = 121 INFO @ Fri, 10 Dec 2021 11:04:45: #1 total tags in treatment: 6275769 INFO @ Fri, 10 Dec 2021 11:04:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:04:45: #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 11:04:45: #1 tags after filtering in treatment: 5838688 INFO @ Fri, 10 Dec 2021 11:04:45: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 11:04:45: #1 finished! INFO @ Fri, 10 Dec 2021 11:04:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:04:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:04:46: 9000000 INFO @ Fri, 10 Dec 2021 11:04:46: #2 number of paired peaks: 4181 INFO @ Fri, 10 Dec 2021 11:04:46: start model_add_line... INFO @ Fri, 10 Dec 2021 11:04:46: start X-correlation... INFO @ Fri, 10 Dec 2021 11:04:46: end of X-cor INFO @ Fri, 10 Dec 2021 11:04:46: #2 finished! INFO @ Fri, 10 Dec 2021 11:04:46: #2 predicted fragment length is 240 bps INFO @ Fri, 10 Dec 2021 11:04:46: #2 alternative fragment length(s) may be 240 bps INFO @ Fri, 10 Dec 2021 11:04:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.05_model.r WARNING @ Fri, 10 Dec 2021 11:04:46: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:04:46: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Fri, 10 Dec 2021 11:04:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:04:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:04:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:04:50: 5000000 INFO @ Fri, 10 Dec 2021 11:04:52: 10000000 INFO @ Fri, 10 Dec 2021 11:04:56: 6000000 INFO @ Fri, 10 Dec 2021 11:04:58: 11000000 INFO @ Fri, 10 Dec 2021 11:05:02: 7000000 INFO @ Fri, 10 Dec 2021 11:05:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:05:05: 12000000 INFO @ Fri, 10 Dec 2021 11:05:09: 8000000 INFO @ Fri, 10 Dec 2021 11:05:11: 13000000 INFO @ Fri, 10 Dec 2021 11:05:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:05:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:05:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.05_summits.bed INFO @ Fri, 10 Dec 2021 11:05:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6382 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:05:15: 9000000 INFO @ Fri, 10 Dec 2021 11:05:17: 14000000 INFO @ Fri, 10 Dec 2021 11:05:18: #1 tag size is determined as 121 bps INFO @ Fri, 10 Dec 2021 11:05:18: #1 tag size = 121 INFO @ Fri, 10 Dec 2021 11:05:18: #1 total tags in treatment: 6275769 INFO @ Fri, 10 Dec 2021 11:05:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:05:18: #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 11:05:18: #1 tags after filtering in treatment: 5838688 INFO @ Fri, 10 Dec 2021 11:05:18: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 11:05:18: #1 finished! INFO @ Fri, 10 Dec 2021 11:05:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:05:18: #2 number of paired peaks: 4181 INFO @ Fri, 10 Dec 2021 11:05:18: start model_add_line... INFO @ Fri, 10 Dec 2021 11:05:19: start X-correlation... INFO @ Fri, 10 Dec 2021 11:05:19: end of X-cor INFO @ Fri, 10 Dec 2021 11:05:19: #2 finished! INFO @ Fri, 10 Dec 2021 11:05:19: #2 predicted fragment length is 240 bps INFO @ Fri, 10 Dec 2021 11:05:19: #2 alternative fragment length(s) may be 240 bps INFO @ Fri, 10 Dec 2021 11:05:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.10_model.r WARNING @ Fri, 10 Dec 2021 11:05:19: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:05:19: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Fri, 10 Dec 2021 11:05:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:05:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:05:21: 10000000 INFO @ Fri, 10 Dec 2021 11:05:27: 11000000 INFO @ Fri, 10 Dec 2021 11:05:33: 12000000 INFO @ Fri, 10 Dec 2021 11:05:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:05:39: 13000000 INFO @ Fri, 10 Dec 2021 11:05:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.10_summits.bed INFO @ Fri, 10 Dec 2021 11:05:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5037 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:05:45: 14000000 INFO @ Fri, 10 Dec 2021 11:05:46: #1 tag size is determined as 121 bps INFO @ Fri, 10 Dec 2021 11:05:46: #1 tag size = 121 INFO @ Fri, 10 Dec 2021 11:05:46: #1 total tags in treatment: 6275769 INFO @ Fri, 10 Dec 2021 11:05:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:05:46: #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 11:05:46: #1 tags after filtering in treatment: 5838688 INFO @ Fri, 10 Dec 2021 11:05:46: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 11:05:46: #1 finished! INFO @ Fri, 10 Dec 2021 11:05:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:05:46: #2 number of paired peaks: 4181 INFO @ Fri, 10 Dec 2021 11:05:46: start model_add_line... INFO @ Fri, 10 Dec 2021 11:05:46: start X-correlation... INFO @ Fri, 10 Dec 2021 11:05:46: end of X-cor INFO @ Fri, 10 Dec 2021 11:05:46: #2 finished! INFO @ Fri, 10 Dec 2021 11:05:46: #2 predicted fragment length is 240 bps INFO @ Fri, 10 Dec 2021 11:05:46: #2 alternative fragment length(s) may be 240 bps INFO @ Fri, 10 Dec 2021 11:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.20_model.r WARNING @ Fri, 10 Dec 2021 11:05:46: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:05:46: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Fri, 10 Dec 2021 11:05:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:05:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:06:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:06:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:06:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:06:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340460/SRX10340460.20_summits.bed INFO @ Fri, 10 Dec 2021 11:06:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3202 records, 4 fields): 5 millis CompletedMACS2peakCalling