Job ID = 14171324 SRX = SRX9005673 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 2660620 READS because READLEN < 1 Read 13483346 spots for SRR12515074/SRR12515074.sra Written 13483346 spots for SRR12515074/SRR12515074.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172015 ("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 16 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] 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] 42 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] 8451168 / 10264953 = 0.8233 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 12:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.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 12:15:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:15:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:16:03: 1000000 INFO @ Sat, 11 Dec 2021 12:16:11: 2000000 INFO @ Sat, 11 Dec 2021 12:16:19: 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 12:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.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 12:16:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:16:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:16:28: 4000000 INFO @ Sat, 11 Dec 2021 12:16:35: 1000000 INFO @ Sat, 11 Dec 2021 12:16:38: 5000000 INFO @ Sat, 11 Dec 2021 12:16:47: 2000000 INFO @ Sat, 11 Dec 2021 12:16:47: 6000000 INFO @ Sat, 11 Dec 2021 12:16:50: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 12:16:50: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 12:16:50: #1 total tags in treatment: 1649286 INFO @ Sat, 11 Dec 2021 12:16:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:16:50: #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 12:16:50: #1 tags after filtering in treatment: 1466836 INFO @ Sat, 11 Dec 2021 12:16:50: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 12:16:50: #1 finished! INFO @ Sat, 11 Dec 2021 12:16:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:16:51: #2 number of paired peaks: 4036 INFO @ Sat, 11 Dec 2021 12:16:51: start model_add_line... INFO @ Sat, 11 Dec 2021 12:16:51: start X-correlation... INFO @ Sat, 11 Dec 2021 12:16:51: end of X-cor INFO @ Sat, 11 Dec 2021 12:16:51: #2 finished! INFO @ Sat, 11 Dec 2021 12:16:51: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 12:16:51: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 12:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.05_model.r WARNING @ Sat, 11 Dec 2021 12:16:51: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:16:51: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 11 Dec 2021 12:16:51: #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 12:16:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:16:51: #3 Pre-compute pvalue-qvalue table... 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 12:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.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 12:16:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:16:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:16:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:16:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:16:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:16:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.05_summits.bed INFO @ Sat, 11 Dec 2021 12:16:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2455 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:16:58: 3000000 INFO @ Sat, 11 Dec 2021 12:17:03: 1000000 INFO @ Sat, 11 Dec 2021 12:17:09: 4000000 INFO @ Sat, 11 Dec 2021 12:17:12: 2000000 INFO @ Sat, 11 Dec 2021 12:17:20: 5000000 INFO @ Sat, 11 Dec 2021 12:17:21: 3000000 INFO @ Sat, 11 Dec 2021 12:17:30: 4000000 INFO @ Sat, 11 Dec 2021 12:17:32: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:17:36: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 12:17:36: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 12:17:36: #1 total tags in treatment: 1649286 INFO @ Sat, 11 Dec 2021 12:17:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:17:36: #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 12:17:36: #1 tags after filtering in treatment: 1466836 INFO @ Sat, 11 Dec 2021 12:17:36: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 12:17:36: #1 finished! INFO @ Sat, 11 Dec 2021 12:17:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:17:36: #2 number of paired peaks: 4036 INFO @ Sat, 11 Dec 2021 12:17:36: start model_add_line... INFO @ Sat, 11 Dec 2021 12:17:36: start X-correlation... INFO @ Sat, 11 Dec 2021 12:17:36: end of X-cor INFO @ Sat, 11 Dec 2021 12:17:36: #2 finished! INFO @ Sat, 11 Dec 2021 12:17:36: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 12:17:36: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 12:17:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.10_model.r WARNING @ Sat, 11 Dec 2021 12:17:36: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:17:36: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 11 Dec 2021 12:17:36: #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 12:17:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:17:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:17:39: 5000000 INFO @ Sat, 11 Dec 2021 12:17:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.10_summits.bed INFO @ Sat, 11 Dec 2021 12:17:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1349 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:17:47: 6000000 INFO @ Sat, 11 Dec 2021 12:17:50: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 12:17:50: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 12:17:50: #1 total tags in treatment: 1649286 INFO @ Sat, 11 Dec 2021 12:17:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:17:50: #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 12:17:50: #1 tags after filtering in treatment: 1466836 INFO @ Sat, 11 Dec 2021 12:17:50: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 11 Dec 2021 12:17:50: #1 finished! INFO @ Sat, 11 Dec 2021 12:17:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:17:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:17:50: #2 number of paired peaks: 4036 INFO @ Sat, 11 Dec 2021 12:17:50: start model_add_line... INFO @ Sat, 11 Dec 2021 12:17:50: start X-correlation... INFO @ Sat, 11 Dec 2021 12:17:50: end of X-cor INFO @ Sat, 11 Dec 2021 12:17:50: #2 finished! INFO @ Sat, 11 Dec 2021 12:17:50: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 12:17:50: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 12:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.20_model.r WARNING @ Sat, 11 Dec 2021 12:17:50: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:17:50: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 11 Dec 2021 12:17:50: #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 12:17:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:17:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:17:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:17:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005673/SRX9005673.20_summits.bed INFO @ Sat, 11 Dec 2021 12:17:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (711 records, 4 fields): 3 millis CompletedMACS2peakCalling