Job ID = 14167165 SRX = SRX10340463 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 990317 READS because READLEN < 1 Read 7677567 spots for SRR13962472/SRR13962472.sra Written 7677567 spots for SRR13962472/SRR13962472.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167732 ("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] 2 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 3 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 4 unmatched pairs [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] 2 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 4 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1190385 / 6047237 = 0.1968 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 11:06:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.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 11:06:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:06:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:06:15: 1000000 INFO @ Fri, 10 Dec 2021 11:06:27: 2000000 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 11:06:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.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 11:06:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:06:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:06:38: 3000000 INFO @ Fri, 10 Dec 2021 11:06:45: 1000000 INFO @ Fri, 10 Dec 2021 11:06:49: 4000000 INFO @ Fri, 10 Dec 2021 11:06:55: 2000000 INFO @ Fri, 10 Dec 2021 11:07:01: 5000000 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 11:07:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.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 11:07:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:07:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:07:05: 3000000 INFO @ Fri, 10 Dec 2021 11:07:13: 6000000 INFO @ Fri, 10 Dec 2021 11:07:16: 1000000 INFO @ Fri, 10 Dec 2021 11:07:16: 4000000 INFO @ Fri, 10 Dec 2021 11:07:24: 7000000 INFO @ Fri, 10 Dec 2021 11:07:27: 2000000 INFO @ Fri, 10 Dec 2021 11:07:27: 5000000 INFO @ Fri, 10 Dec 2021 11:07:36: 8000000 INFO @ Fri, 10 Dec 2021 11:07:37: 3000000 INFO @ Fri, 10 Dec 2021 11:07:37: 6000000 INFO @ Fri, 10 Dec 2021 11:07:47: 4000000 INFO @ Fri, 10 Dec 2021 11:07:47: 9000000 INFO @ Fri, 10 Dec 2021 11:07:48: 7000000 INFO @ Fri, 10 Dec 2021 11:07:58: 8000000 INFO @ Fri, 10 Dec 2021 11:07:58: 5000000 INFO @ Fri, 10 Dec 2021 11:07:59: 10000000 INFO @ Fri, 10 Dec 2021 11:08:06: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:08:06: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:08:06: #1 total tags in treatment: 4645357 INFO @ Fri, 10 Dec 2021 11:08:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:06: #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 11:08:07: #1 tags after filtering in treatment: 4563831 INFO @ Fri, 10 Dec 2021 11:08:07: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:08:07: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:08:07: #2 number of paired peaks: 251 WARNING @ Fri, 10 Dec 2021 11:08:07: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 10 Dec 2021 11:08:07: start model_add_line... INFO @ Fri, 10 Dec 2021 11:08:07: start X-correlation... INFO @ Fri, 10 Dec 2021 11:08:07: end of X-cor INFO @ Fri, 10 Dec 2021 11:08:07: #2 finished! INFO @ Fri, 10 Dec 2021 11:08:07: #2 predicted fragment length is 226 bps INFO @ Fri, 10 Dec 2021 11:08:07: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 10 Dec 2021 11:08:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.05_model.r WARNING @ Fri, 10 Dec 2021 11:08:07: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:08:07: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Fri, 10 Dec 2021 11:08:07: #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 11:08:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:08:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:08:08: 6000000 INFO @ Fri, 10 Dec 2021 11:08:09: 9000000 INFO @ Fri, 10 Dec 2021 11:08:19: 7000000 INFO @ Fri, 10 Dec 2021 11:08:19: 10000000 INFO @ Fri, 10 Dec 2021 11:08:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:08:26: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:08:26: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:08:26: #1 total tags in treatment: 4645357 INFO @ Fri, 10 Dec 2021 11:08:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:26: #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 11:08:26: #1 tags after filtering in treatment: 4563831 INFO @ Fri, 10 Dec 2021 11:08:26: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:08:26: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:08:26: #2 number of paired peaks: 251 WARNING @ Fri, 10 Dec 2021 11:08:26: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 10 Dec 2021 11:08:26: start model_add_line... INFO @ Fri, 10 Dec 2021 11:08:26: start X-correlation... INFO @ Fri, 10 Dec 2021 11:08:26: end of X-cor INFO @ Fri, 10 Dec 2021 11:08:26: #2 finished! INFO @ Fri, 10 Dec 2021 11:08:26: #2 predicted fragment length is 226 bps INFO @ Fri, 10 Dec 2021 11:08:26: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 10 Dec 2021 11:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.10_model.r WARNING @ Fri, 10 Dec 2021 11:08:26: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:08:26: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Fri, 10 Dec 2021 11:08:26: #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 11:08:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:08:29: 8000000 INFO @ Fri, 10 Dec 2021 11:08:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:08:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:08:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.05_summits.bed INFO @ Fri, 10 Dec 2021 11:08:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1597 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:08:38: 9000000 INFO @ Fri, 10 Dec 2021 11:08:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:08:48: 10000000 INFO @ Fri, 10 Dec 2021 11:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.10_summits.bed INFO @ Fri, 10 Dec 2021 11:08:48: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (670 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:08:54: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 11:08:54: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 11:08:54: #1 total tags in treatment: 4645357 INFO @ Fri, 10 Dec 2021 11:08:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:54: #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 11:08:55: #1 tags after filtering in treatment: 4563831 INFO @ Fri, 10 Dec 2021 11:08:55: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 10 Dec 2021 11:08:55: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:08:55: #2 number of paired peaks: 251 WARNING @ Fri, 10 Dec 2021 11:08:55: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 10 Dec 2021 11:08:55: start model_add_line... INFO @ Fri, 10 Dec 2021 11:08:55: start X-correlation... INFO @ Fri, 10 Dec 2021 11:08:55: end of X-cor INFO @ Fri, 10 Dec 2021 11:08:55: #2 finished! INFO @ Fri, 10 Dec 2021 11:08:55: #2 predicted fragment length is 226 bps INFO @ Fri, 10 Dec 2021 11:08:55: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 10 Dec 2021 11:08:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.20_model.r WARNING @ Fri, 10 Dec 2021 11:08:55: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:08:55: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Fri, 10 Dec 2021 11:08:55: #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 11:08:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:08:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:09:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:09:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:09:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:09:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340463/SRX10340463.20_summits.bed INFO @ Fri, 10 Dec 2021 11:09:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling