Job ID = 14171268 SRX = SRX9005656 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 599446 READS because READLEN < 1 Read 6761452 spots for SRR12515057/SRR12515057.sra Written 6761452 spots for SRR12515057/SRR12515057.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171744 ("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] 4 unmatched pairs [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] 1 unmatched pairs [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] 8 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 704972 / 5498312 = 0.1282 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 11:10:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.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 11:10:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:10:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:10:10: 1000000 INFO @ Sat, 11 Dec 2021 11:10:18: 2000000 INFO @ Sat, 11 Dec 2021 11:10:26: 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 11:10:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.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 11:10:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:10:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:10:34: 4000000 INFO @ Sat, 11 Dec 2021 11:10:39: 1000000 INFO @ Sat, 11 Dec 2021 11:10:43: 5000000 INFO @ Sat, 11 Dec 2021 11:10:47: 2000000 INFO @ Sat, 11 Dec 2021 11:10:51: 6000000 INFO @ Sat, 11 Dec 2021 11:10:54: 3000000 INFO @ Sat, 11 Dec 2021 11:11:00: 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 @ Sat, 11 Dec 2021 11:11:01: 4000000 INFO @ Sat, 11 Dec 2021 11:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.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 11:11:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:11:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:11:08: 5000000 INFO @ Sat, 11 Dec 2021 11:11:08: 8000000 INFO @ Sat, 11 Dec 2021 11:11:11: 1000000 INFO @ Sat, 11 Dec 2021 11:11:16: 6000000 INFO @ Sat, 11 Dec 2021 11:11:17: 9000000 INFO @ Sat, 11 Dec 2021 11:11:19: 2000000 INFO @ Sat, 11 Dec 2021 11:11:23: 7000000 INFO @ Sat, 11 Dec 2021 11:11:26: 10000000 INFO @ Sat, 11 Dec 2021 11:11:28: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:11:28: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:11:28: #1 total tags in treatment: 4694929 INFO @ Sat, 11 Dec 2021 11:11:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:11:28: #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 11:11:28: #1 tags after filtering in treatment: 3632136 INFO @ Sat, 11 Dec 2021 11:11:28: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 11:11:28: #1 finished! INFO @ Sat, 11 Dec 2021 11:11:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:11:28: 3000000 INFO @ Sat, 11 Dec 2021 11:11:28: #2 number of paired peaks: 7378 INFO @ Sat, 11 Dec 2021 11:11:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:11:29: start X-correlation... INFO @ Sat, 11 Dec 2021 11:11:29: end of X-cor INFO @ Sat, 11 Dec 2021 11:11:29: #2 finished! INFO @ Sat, 11 Dec 2021 11:11:29: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 11:11:29: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 11:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.05_model.r WARNING @ Sat, 11 Dec 2021 11:11:29: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:11:29: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 11:11:29: #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 11:11:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:11:30: 8000000 INFO @ Sat, 11 Dec 2021 11:11:36: 4000000 INFO @ Sat, 11 Dec 2021 11:11:37: 9000000 INFO @ Sat, 11 Dec 2021 11:11:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:11:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:11:45: 5000000 INFO @ Sat, 11 Dec 2021 11:11:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:11:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.05_summits.bed INFO @ Sat, 11 Dec 2021 11:11:45: Done! INFO @ Sat, 11 Dec 2021 11:11:45: 10000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8675 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:11:47: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:11:47: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:11:47: #1 total tags in treatment: 4694929 INFO @ Sat, 11 Dec 2021 11:11:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:11:47: #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 11:11:47: #1 tags after filtering in treatment: 3632136 INFO @ Sat, 11 Dec 2021 11:11:47: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 11:11:47: #1 finished! INFO @ Sat, 11 Dec 2021 11:11:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:11:47: #2 number of paired peaks: 7378 INFO @ Sat, 11 Dec 2021 11:11:47: start model_add_line... INFO @ Sat, 11 Dec 2021 11:11:47: start X-correlation... INFO @ Sat, 11 Dec 2021 11:11:47: end of X-cor INFO @ Sat, 11 Dec 2021 11:11:47: #2 finished! INFO @ Sat, 11 Dec 2021 11:11:47: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 11:11:47: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 11:11:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.10_model.r WARNING @ Sat, 11 Dec 2021 11:11:47: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:11:47: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 11:11:47: #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 11:11:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:11:47: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:11:53: 6000000 INFO @ Sat, 11 Dec 2021 11:11:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:12:01: 7000000 INFO @ Sat, 11 Dec 2021 11:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.10_summits.bed INFO @ Sat, 11 Dec 2021 11:12:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6927 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:12:09: 8000000 INFO @ Sat, 11 Dec 2021 11:12:17: 9000000 INFO @ Sat, 11 Dec 2021 11:12:25: 10000000 INFO @ Sat, 11 Dec 2021 11:12:27: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:12:27: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:12:27: #1 total tags in treatment: 4694929 INFO @ Sat, 11 Dec 2021 11:12:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:12:27: #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 11:12:27: #1 tags after filtering in treatment: 3632136 INFO @ Sat, 11 Dec 2021 11:12:27: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 11:12:27: #1 finished! INFO @ Sat, 11 Dec 2021 11:12:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:12:28: #2 number of paired peaks: 7378 INFO @ Sat, 11 Dec 2021 11:12:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:12:28: start X-correlation... INFO @ Sat, 11 Dec 2021 11:12:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:12:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:12:28: #2 predicted fragment length is 221 bps INFO @ Sat, 11 Dec 2021 11:12:28: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 11 Dec 2021 11:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.20_model.r WARNING @ Sat, 11 Dec 2021 11:12:28: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:12:28: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Sat, 11 Dec 2021 11:12:28: #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 11:12:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:12:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005656/SRX9005656.20_summits.bed INFO @ Sat, 11 Dec 2021 11:12:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4829 records, 4 fields): 6 millis CompletedMACS2peakCalling