Job ID = 14167164 SRX = SRX10340462 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1209696 READS because READLEN < 1 Read 11111822 spots for SRR13962471/SRR13962471.sra Written 11111822 spots for SRR13962471/SRR13962471.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167737 ("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] 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] 1 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 6 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] 1 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 6 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1999293 / 8617683 = 0.2320 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 11:07:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.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 11:07:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:32: 1000000 INFO @ Fri, 10 Dec 2021 11:07:39: 2000000 INFO @ Fri, 10 Dec 2021 11:07:47: 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 11:07:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.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 11:07:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:54: 4000000 INFO @ Fri, 10 Dec 2021 11:08:03: 1000000 INFO @ Fri, 10 Dec 2021 11:08:04: 5000000 INFO @ Fri, 10 Dec 2021 11:08:13: 2000000 INFO @ Fri, 10 Dec 2021 11:08:13: 6000000 INFO @ Fri, 10 Dec 2021 11:08:22: 3000000 INFO @ Fri, 10 Dec 2021 11:08:22: 7000000 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 11:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.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 11:08:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:08:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:08:31: 8000000 INFO @ Fri, 10 Dec 2021 11:08:31: 4000000 INFO @ Fri, 10 Dec 2021 11:08:35: 1000000 INFO @ Fri, 10 Dec 2021 11:08:41: 9000000 INFO @ Fri, 10 Dec 2021 11:08:41: 5000000 INFO @ Fri, 10 Dec 2021 11:08:45: 2000000 INFO @ Fri, 10 Dec 2021 11:08:51: 10000000 INFO @ Fri, 10 Dec 2021 11:08:52: 6000000 INFO @ Fri, 10 Dec 2021 11:08:56: 3000000 INFO @ Fri, 10 Dec 2021 11:09:01: 11000000 INFO @ Fri, 10 Dec 2021 11:09:02: 7000000 INFO @ Fri, 10 Dec 2021 11:09:06: 4000000 INFO @ Fri, 10 Dec 2021 11:09:12: 12000000 INFO @ Fri, 10 Dec 2021 11:09:12: 8000000 INFO @ Fri, 10 Dec 2021 11:09:17: 5000000 INFO @ Fri, 10 Dec 2021 11:09:22: 9000000 INFO @ Fri, 10 Dec 2021 11:09:22: 13000000 INFO @ Fri, 10 Dec 2021 11:09:28: 6000000 INFO @ Fri, 10 Dec 2021 11:09:32: 10000000 INFO @ Fri, 10 Dec 2021 11:09:32: 14000000 INFO @ Fri, 10 Dec 2021 11:09:37: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:09:37: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:09:37: #1 total tags in treatment: 6168588 INFO @ Fri, 10 Dec 2021 11:09:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:09:37: #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 11:09:37: #1 tags after filtering in treatment: 6034478 INFO @ Fri, 10 Dec 2021 11:09:37: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:09:37: #1 finished! INFO @ Fri, 10 Dec 2021 11:09:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:09:38: #2 number of paired peaks: 167 WARNING @ Fri, 10 Dec 2021 11:09:38: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 10 Dec 2021 11:09:38: start model_add_line... INFO @ Fri, 10 Dec 2021 11:09:38: start X-correlation... INFO @ Fri, 10 Dec 2021 11:09:38: end of X-cor INFO @ Fri, 10 Dec 2021 11:09:38: #2 finished! INFO @ Fri, 10 Dec 2021 11:09:38: #2 predicted fragment length is 222 bps INFO @ Fri, 10 Dec 2021 11:09:38: #2 alternative fragment length(s) may be 222 bps INFO @ Fri, 10 Dec 2021 11:09:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.05_model.r WARNING @ Fri, 10 Dec 2021 11:09:38: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:09:38: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Fri, 10 Dec 2021 11:09:38: #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 11:09:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:09:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:09:38: 7000000 INFO @ Fri, 10 Dec 2021 11:09:41: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:09:49: 8000000 INFO @ Fri, 10 Dec 2021 11:09:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:09:51: 12000000 INFO @ Fri, 10 Dec 2021 11:09:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:09:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:09:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.05_summits.bed INFO @ Fri, 10 Dec 2021 11:09:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (732 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:09:59: 9000000 INFO @ Fri, 10 Dec 2021 11:10:01: 13000000 INFO @ Fri, 10 Dec 2021 11:10:10: 10000000 INFO @ Fri, 10 Dec 2021 11:10:11: 14000000 INFO @ Fri, 10 Dec 2021 11:10:16: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:10:16: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:10:16: #1 total tags in treatment: 6168588 INFO @ Fri, 10 Dec 2021 11:10:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:10:16: #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 11:10:16: #1 tags after filtering in treatment: 6034478 INFO @ Fri, 10 Dec 2021 11:10:16: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:10:16: #1 finished! INFO @ Fri, 10 Dec 2021 11:10:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:10:16: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:10:17: #2 number of paired peaks: 167 WARNING @ Fri, 10 Dec 2021 11:10:17: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 10 Dec 2021 11:10:17: start model_add_line... INFO @ Fri, 10 Dec 2021 11:10:17: start X-correlation... INFO @ Fri, 10 Dec 2021 11:10:17: end of X-cor INFO @ Fri, 10 Dec 2021 11:10:17: #2 finished! INFO @ Fri, 10 Dec 2021 11:10:17: #2 predicted fragment length is 222 bps INFO @ Fri, 10 Dec 2021 11:10:17: #2 alternative fragment length(s) may be 222 bps INFO @ Fri, 10 Dec 2021 11:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.10_model.r WARNING @ Fri, 10 Dec 2021 11:10:17: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:10:17: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Fri, 10 Dec 2021 11:10:17: #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 11:10:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:10:20: 11000000 INFO @ Fri, 10 Dec 2021 11:10:29: 12000000 INFO @ Fri, 10 Dec 2021 11:10:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.10_summits.bed INFO @ Fri, 10 Dec 2021 11:10:36: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:10:38: 13000000 INFO @ Fri, 10 Dec 2021 11:10:48: 14000000 INFO @ Fri, 10 Dec 2021 11:10:53: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:10:53: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:10:53: #1 total tags in treatment: 6168588 INFO @ Fri, 10 Dec 2021 11:10:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:10:53: #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 11:10:53: #1 tags after filtering in treatment: 6034478 INFO @ Fri, 10 Dec 2021 11:10:53: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:10:53: #1 finished! INFO @ Fri, 10 Dec 2021 11:10:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:10:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:10:53: #2 number of paired peaks: 167 WARNING @ Fri, 10 Dec 2021 11:10:53: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 10 Dec 2021 11:10:53: start model_add_line... INFO @ Fri, 10 Dec 2021 11:10:53: start X-correlation... INFO @ Fri, 10 Dec 2021 11:10:53: end of X-cor INFO @ Fri, 10 Dec 2021 11:10:53: #2 finished! INFO @ Fri, 10 Dec 2021 11:10:53: #2 predicted fragment length is 222 bps INFO @ Fri, 10 Dec 2021 11:10:53: #2 alternative fragment length(s) may be 222 bps INFO @ Fri, 10 Dec 2021 11:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.20_model.r WARNING @ Fri, 10 Dec 2021 11:10:53: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:10:53: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Fri, 10 Dec 2021 11:10:53: #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 11:10:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:10:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:11:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:11:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:11:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:11:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340462/SRX10340462.20_summits.bed INFO @ Fri, 10 Dec 2021 11:11:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (108 records, 4 fields): 2 millis CompletedMACS2peakCalling