Job ID = 14171345 SRX = SRX9005681 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 597069 READS because READLEN < 1 Read 7009567 spots for SRR12515082/SRR12515082.sra Written 7009567 spots for SRR12515082/SRR12515082.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171894 ("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] 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] 6 unmatched pairs [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] 829492 / 6025329 = 0.1377 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 @ Sat, 11 Dec 2021 11:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.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 11:45:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:45:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:45:57: 1000000 INFO @ Sat, 11 Dec 2021 11:46:05: 2000000 INFO @ Sat, 11 Dec 2021 11:46:13: 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 @ Sat, 11 Dec 2021 11:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.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 11:46:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:21: 4000000 INFO @ Sat, 11 Dec 2021 11:46:29: 1000000 INFO @ Sat, 11 Dec 2021 11:46:31: 5000000 INFO @ Sat, 11 Dec 2021 11:46:38: 2000000 INFO @ Sat, 11 Dec 2021 11:46:40: 6000000 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 11:46:48: 3000000 INFO @ Sat, 11 Dec 2021 11:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.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 11:46:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:46:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:46:49: 7000000 INFO @ Sat, 11 Dec 2021 11:46:58: 4000000 INFO @ Sat, 11 Dec 2021 11:46:58: 1000000 INFO @ Sat, 11 Dec 2021 11:46:59: 8000000 INFO @ Sat, 11 Dec 2021 11:47:07: 5000000 INFO @ Sat, 11 Dec 2021 11:47:08: 2000000 INFO @ Sat, 11 Dec 2021 11:47:08: 9000000 INFO @ Sat, 11 Dec 2021 11:47:17: 6000000 INFO @ Sat, 11 Dec 2021 11:47:18: 3000000 INFO @ Sat, 11 Dec 2021 11:47:18: 10000000 INFO @ Sat, 11 Dec 2021 11:47:27: 7000000 INFO @ Sat, 11 Dec 2021 11:47:28: 11000000 INFO @ Sat, 11 Dec 2021 11:47:28: 4000000 INFO @ Sat, 11 Dec 2021 11:47:28: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:47:28: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:47:28: #1 total tags in treatment: 5162260 INFO @ Sat, 11 Dec 2021 11:47:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:47:28: #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 11:47:29: #1 tags after filtering in treatment: 5025336 INFO @ Sat, 11 Dec 2021 11:47:29: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:47:29: #1 finished! INFO @ Sat, 11 Dec 2021 11:47:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:47:29: #2 number of paired peaks: 547 WARNING @ Sat, 11 Dec 2021 11:47:29: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Sat, 11 Dec 2021 11:47:29: start model_add_line... INFO @ Sat, 11 Dec 2021 11:47:29: start X-correlation... INFO @ Sat, 11 Dec 2021 11:47:29: end of X-cor INFO @ Sat, 11 Dec 2021 11:47:29: #2 finished! INFO @ Sat, 11 Dec 2021 11:47:29: #2 predicted fragment length is 248 bps INFO @ Sat, 11 Dec 2021 11:47:29: #2 alternative fragment length(s) may be 248 bps INFO @ Sat, 11 Dec 2021 11:47:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.05_model.r WARNING @ Sat, 11 Dec 2021 11:47:29: #2 Since the d (248) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:47:29: #2 You may need to consider one of the other alternative d(s): 248 WARNING @ Sat, 11 Dec 2021 11:47:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:47:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:47:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:47:37: 8000000 INFO @ Sat, 11 Dec 2021 11:47:38: 5000000 INFO @ Sat, 11 Dec 2021 11:47:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:47:46: 9000000 INFO @ Sat, 11 Dec 2021 11:47:47: 6000000 INFO @ Sat, 11 Dec 2021 11:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.05_summits.bed INFO @ Sat, 11 Dec 2021 11:47:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1731 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:47:56: 10000000 INFO @ Sat, 11 Dec 2021 11:47:57: 7000000 INFO @ Sat, 11 Dec 2021 11:48:06: 11000000 INFO @ Sat, 11 Dec 2021 11:48:06: 8000000 INFO @ Sat, 11 Dec 2021 11:48:06: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:48:06: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:48:06: #1 total tags in treatment: 5162260 INFO @ Sat, 11 Dec 2021 11:48:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:48:06: #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 11:48:06: #1 tags after filtering in treatment: 5025336 INFO @ Sat, 11 Dec 2021 11:48:06: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:48:06: #1 finished! INFO @ Sat, 11 Dec 2021 11:48:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:48:07: #2 number of paired peaks: 547 WARNING @ Sat, 11 Dec 2021 11:48:07: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Sat, 11 Dec 2021 11:48:07: start model_add_line... INFO @ Sat, 11 Dec 2021 11:48:07: start X-correlation... INFO @ Sat, 11 Dec 2021 11:48:07: end of X-cor INFO @ Sat, 11 Dec 2021 11:48:07: #2 finished! INFO @ Sat, 11 Dec 2021 11:48:07: #2 predicted fragment length is 248 bps INFO @ Sat, 11 Dec 2021 11:48:07: #2 alternative fragment length(s) may be 248 bps INFO @ Sat, 11 Dec 2021 11:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.10_model.r WARNING @ Sat, 11 Dec 2021 11:48:07: #2 Since the d (248) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:48:07: #2 You may need to consider one of the other alternative d(s): 248 WARNING @ Sat, 11 Dec 2021 11:48:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:48:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:48:14: 9000000 INFO @ Sat, 11 Dec 2021 11:48:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:48:23: 10000000 INFO @ Sat, 11 Dec 2021 11:48:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:48:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:48:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.10_summits.bed INFO @ Sat, 11 Dec 2021 11:48:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (882 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:48:31: 11000000 INFO @ Sat, 11 Dec 2021 11:48:32: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:48:32: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:48:32: #1 total tags in treatment: 5162260 INFO @ Sat, 11 Dec 2021 11:48:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:48:32: #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 11:48:32: #1 tags after filtering in treatment: 5025336 INFO @ Sat, 11 Dec 2021 11:48:32: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:48:32: #1 finished! INFO @ Sat, 11 Dec 2021 11:48:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:48:32: #2 number of paired peaks: 547 WARNING @ Sat, 11 Dec 2021 11:48:32: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Sat, 11 Dec 2021 11:48:32: start model_add_line... INFO @ Sat, 11 Dec 2021 11:48:32: start X-correlation... INFO @ Sat, 11 Dec 2021 11:48:32: end of X-cor INFO @ Sat, 11 Dec 2021 11:48:32: #2 finished! INFO @ Sat, 11 Dec 2021 11:48:32: #2 predicted fragment length is 248 bps INFO @ Sat, 11 Dec 2021 11:48:32: #2 alternative fragment length(s) may be 248 bps INFO @ Sat, 11 Dec 2021 11:48:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.20_model.r WARNING @ Sat, 11 Dec 2021 11:48:32: #2 Since the d (248) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:48:32: #2 You may need to consider one of the other alternative d(s): 248 WARNING @ Sat, 11 Dec 2021 11:48:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:48:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:48:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:48:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005681/SRX9005681.20_summits.bed INFO @ Sat, 11 Dec 2021 11:48:50: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (415 records, 4 fields): 2 millis CompletedMACS2peakCalling