Job ID = 14167169 SRX = SRX10340467 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 996869 READS because READLEN < 1 Read 7104357 spots for SRR13962476/SRR13962476.sra Written 7104357 spots for SRR13962476/SRR13962476.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167713 ("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 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 5 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 1 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] 3 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1240417 / 5068242 = 0.2447 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 10:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.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 10:59:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:59:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:59:59: 1000000 INFO @ Fri, 10 Dec 2021 11:00:06: 2000000 INFO @ Fri, 10 Dec 2021 11:00:13: 3000000 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 11:00:21: 4000000 INFO @ Fri, 10 Dec 2021 11:00:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.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 11:00:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:28: 5000000 INFO @ Fri, 10 Dec 2021 11:00:30: 1000000 INFO @ Fri, 10 Dec 2021 11:00:36: 6000000 INFO @ Fri, 10 Dec 2021 11:00:38: 2000000 INFO @ Fri, 10 Dec 2021 11:00:44: 7000000 INFO @ Fri, 10 Dec 2021 11:00:46: 3000000 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 11:00:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.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 11:00:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:52: 8000000 INFO @ Fri, 10 Dec 2021 11:00:54: 4000000 INFO @ Fri, 10 Dec 2021 11:00:56: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:00:56: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:00:56: #1 total tags in treatment: 3677607 INFO @ Fri, 10 Dec 2021 11:00:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:00:56: #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 11:00:56: #1 tags after filtering in treatment: 3596825 INFO @ Fri, 10 Dec 2021 11:00:56: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:00:56: #1 finished! INFO @ Fri, 10 Dec 2021 11:00:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:00:57: #2 number of paired peaks: 2067 INFO @ Fri, 10 Dec 2021 11:00:57: start model_add_line... INFO @ Fri, 10 Dec 2021 11:00:57: start X-correlation... INFO @ Fri, 10 Dec 2021 11:00:57: end of X-cor INFO @ Fri, 10 Dec 2021 11:00:57: #2 finished! INFO @ Fri, 10 Dec 2021 11:00:57: #2 predicted fragment length is 246 bps INFO @ Fri, 10 Dec 2021 11:00:57: #2 alternative fragment length(s) may be 246 bps INFO @ Fri, 10 Dec 2021 11:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.05_model.r WARNING @ Fri, 10 Dec 2021 11:00:57: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:00:57: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Fri, 10 Dec 2021 11:00:57: #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 11:00:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:01:01: 1000000 INFO @ Fri, 10 Dec 2021 11:01:02: 5000000 INFO @ Fri, 10 Dec 2021 11:01:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:01:10: 2000000 INFO @ Fri, 10 Dec 2021 11:01:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:01:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:01:11: 6000000 INFO @ Fri, 10 Dec 2021 11:01:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.05_summits.bed INFO @ Fri, 10 Dec 2021 11:01:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4356 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:01:19: 7000000 INFO @ Fri, 10 Dec 2021 11:01:20: 3000000 INFO @ Fri, 10 Dec 2021 11:01:28: 8000000 INFO @ Fri, 10 Dec 2021 11:01:29: 4000000 INFO @ Fri, 10 Dec 2021 11:01:32: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:01:32: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:01:32: #1 total tags in treatment: 3677607 INFO @ Fri, 10 Dec 2021 11:01:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:01:32: #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 11:01:32: #1 tags after filtering in treatment: 3596825 INFO @ Fri, 10 Dec 2021 11:01:32: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:01:32: #1 finished! INFO @ Fri, 10 Dec 2021 11:01:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:01:33: #2 number of paired peaks: 2067 INFO @ Fri, 10 Dec 2021 11:01:33: start model_add_line... INFO @ Fri, 10 Dec 2021 11:01:33: start X-correlation... INFO @ Fri, 10 Dec 2021 11:01:33: end of X-cor INFO @ Fri, 10 Dec 2021 11:01:33: #2 finished! INFO @ Fri, 10 Dec 2021 11:01:33: #2 predicted fragment length is 246 bps INFO @ Fri, 10 Dec 2021 11:01:33: #2 alternative fragment length(s) may be 246 bps INFO @ Fri, 10 Dec 2021 11:01:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.10_model.r WARNING @ Fri, 10 Dec 2021 11:01:33: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:01:33: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Fri, 10 Dec 2021 11:01:33: #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 11:01:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:01:38: 5000000 INFO @ Fri, 10 Dec 2021 11:01:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:01:46: 6000000 INFO @ Fri, 10 Dec 2021 11:01:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:01:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:01:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.10_summits.bed INFO @ Fri, 10 Dec 2021 11:01:46: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2449 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:01:55: 7000000 INFO @ Fri, 10 Dec 2021 11:02:03: 8000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:02:08: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:02:08: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:02:08: #1 total tags in treatment: 3677607 INFO @ Fri, 10 Dec 2021 11:02:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:08: #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 11:02:08: #1 tags after filtering in treatment: 3596825 INFO @ Fri, 10 Dec 2021 11:02:08: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:02:08: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:08: #2 number of paired peaks: 2067 INFO @ Fri, 10 Dec 2021 11:02:08: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:08: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:08: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:08: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:08: #2 predicted fragment length is 246 bps INFO @ Fri, 10 Dec 2021 11:02:08: #2 alternative fragment length(s) may be 246 bps INFO @ Fri, 10 Dec 2021 11:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.20_model.r WARNING @ Fri, 10 Dec 2021 11:02:08: #2 Since the d (246) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:08: #2 You may need to consider one of the other alternative d(s): 246 WARNING @ Fri, 10 Dec 2021 11:02:08: #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 11:02:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:02:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340467/SRX10340467.20_summits.bed INFO @ Fri, 10 Dec 2021 11:02:21: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (822 records, 4 fields): 3 millis CompletedMACS2peakCalling