Job ID = 14171331 SRX = SRX9005679 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1454265 READS because READLEN < 1 Read 12848341 spots for SRR12515080/SRR12515080.sra Written 12848341 spots for SRR12515080/SRR12515080.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171880 ("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] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 2 unmatched pairs [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] processing reference chrX... [bam_rmdup_core] 3 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2048242 / 10196971 = 0.2009 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 11:48:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.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 11:48:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:48:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:03: 1000000 INFO @ Sat, 11 Dec 2021 11:49:10: 2000000 INFO @ Sat, 11 Dec 2021 11:49:18: 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 11:49:25: 4000000 INFO @ Sat, 11 Dec 2021 11:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.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 11:49:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:49:35: 5000000 INFO @ Sat, 11 Dec 2021 11:49:37: 1000000 INFO @ Sat, 11 Dec 2021 11:49:45: 6000000 INFO @ Sat, 11 Dec 2021 11:49:48: 2000000 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 11:49:55: 7000000 INFO @ Sat, 11 Dec 2021 11:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.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 11:49:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:49:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:50:00: 3000000 INFO @ Sat, 11 Dec 2021 11:50:05: 8000000 INFO @ Sat, 11 Dec 2021 11:50:05: 1000000 INFO @ Sat, 11 Dec 2021 11:50:11: 4000000 INFO @ Sat, 11 Dec 2021 11:50:15: 9000000 INFO @ Sat, 11 Dec 2021 11:50:15: 2000000 INFO @ Sat, 11 Dec 2021 11:50:23: 5000000 INFO @ Sat, 11 Dec 2021 11:50:25: 10000000 INFO @ Sat, 11 Dec 2021 11:50:26: 3000000 INFO @ Sat, 11 Dec 2021 11:50:34: 6000000 INFO @ Sat, 11 Dec 2021 11:50:35: 11000000 INFO @ Sat, 11 Dec 2021 11:50:36: 4000000 INFO @ Sat, 11 Dec 2021 11:50:45: 12000000 INFO @ Sat, 11 Dec 2021 11:50:46: 7000000 INFO @ Sat, 11 Dec 2021 11:50:46: 5000000 INFO @ Sat, 11 Dec 2021 11:50:55: 13000000 INFO @ Sat, 11 Dec 2021 11:50:56: 6000000 INFO @ Sat, 11 Dec 2021 11:50:57: 8000000 INFO @ Sat, 11 Dec 2021 11:51:06: 14000000 INFO @ Sat, 11 Dec 2021 11:51:06: 7000000 INFO @ Sat, 11 Dec 2021 11:51:08: 9000000 INFO @ Sat, 11 Dec 2021 11:51:16: 15000000 INFO @ Sat, 11 Dec 2021 11:51:16: 8000000 INFO @ Sat, 11 Dec 2021 11:51:20: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:51:26: 16000000 INFO @ Sat, 11 Dec 2021 11:51:26: 9000000 INFO @ Sat, 11 Dec 2021 11:51:31: 11000000 INFO @ Sat, 11 Dec 2021 11:51:36: 17000000 INFO @ Sat, 11 Dec 2021 11:51:36: 10000000 INFO @ Sat, 11 Dec 2021 11:51:43: 12000000 INFO @ Sat, 11 Dec 2021 11:51:43: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:51:43: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:51:43: #1 total tags in treatment: 8044420 INFO @ Sat, 11 Dec 2021 11:51:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:51:43: #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 11:51:44: #1 tags after filtering in treatment: 6846557 INFO @ Sat, 11 Dec 2021 11:51:44: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:51:44: #1 finished! INFO @ Sat, 11 Dec 2021 11:51:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:51:44: #2 number of paired peaks: 5255 INFO @ Sat, 11 Dec 2021 11:51:44: start model_add_line... INFO @ Sat, 11 Dec 2021 11:51:44: start X-correlation... INFO @ Sat, 11 Dec 2021 11:51:44: end of X-cor INFO @ Sat, 11 Dec 2021 11:51:44: #2 finished! INFO @ Sat, 11 Dec 2021 11:51:44: #2 predicted fragment length is 305 bps INFO @ Sat, 11 Dec 2021 11:51:44: #2 alternative fragment length(s) may be 305 bps INFO @ Sat, 11 Dec 2021 11:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.05_model.r INFO @ Sat, 11 Dec 2021 11:51:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:51:46: 11000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:51:54: 13000000 INFO @ Sat, 11 Dec 2021 11:51:56: 12000000 INFO @ Sat, 11 Dec 2021 11:52:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:52:06: 14000000 INFO @ Sat, 11 Dec 2021 11:52:06: 13000000 INFO @ Sat, 11 Dec 2021 11:52:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:52:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:52:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.05_summits.bed INFO @ Sat, 11 Dec 2021 11:52:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7789 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:52:16: 14000000 INFO @ Sat, 11 Dec 2021 11:52:17: 15000000 INFO @ Sat, 11 Dec 2021 11:52:26: 15000000 INFO @ Sat, 11 Dec 2021 11:52:29: 16000000 INFO @ Sat, 11 Dec 2021 11:52:35: 16000000 INFO @ Sat, 11 Dec 2021 11:52:40: 17000000 INFO @ Sat, 11 Dec 2021 11:52:45: 17000000 INFO @ Sat, 11 Dec 2021 11:52:48: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:52:48: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:52:48: #1 total tags in treatment: 8044420 INFO @ Sat, 11 Dec 2021 11:52:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:48: #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 11:52:48: #1 tags after filtering in treatment: 6846557 INFO @ Sat, 11 Dec 2021 11:52:48: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:52:48: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:49: #2 number of paired peaks: 5255 INFO @ Sat, 11 Dec 2021 11:52:49: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:49: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:49: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:49: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:49: #2 predicted fragment length is 305 bps INFO @ Sat, 11 Dec 2021 11:52:49: #2 alternative fragment length(s) may be 305 bps INFO @ Sat, 11 Dec 2021 11:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.10_model.r INFO @ Sat, 11 Dec 2021 11:52:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:52: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:52:52: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:52:52: #1 total tags in treatment: 8044420 INFO @ Sat, 11 Dec 2021 11:52:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:52: #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 11:52:52: #1 tags after filtering in treatment: 6846557 INFO @ Sat, 11 Dec 2021 11:52:52: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 11:52:52: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:53: #2 number of paired peaks: 5255 INFO @ Sat, 11 Dec 2021 11:52:53: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:53: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:53: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:53: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:53: #2 predicted fragment length is 305 bps INFO @ Sat, 11 Dec 2021 11:52:53: #2 alternative fragment length(s) may be 305 bps INFO @ Sat, 11 Dec 2021 11:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.20_model.r INFO @ Sat, 11 Dec 2021 11:52:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.10_summits.bed INFO @ Sat, 11 Dec 2021 11:53:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6155 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005679/SRX9005679.20_summits.bed INFO @ Sat, 11 Dec 2021 11:53:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4243 records, 4 fields): 5 millis CompletedMACS2peakCalling