Job ID = 14171379 SRX = SRX9005690 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 621971 READS because READLEN < 1 Read 8563618 spots for SRR12515091/SRR12515091.sra Written 8563618 spots for SRR12515091/SRR12515091.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171961 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 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] 8 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 12 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 16 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 18 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] 1 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 5 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 3138302 / 7118818 = 0.4408 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 11:57:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.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 11:57:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:57:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:57:21: 1000000 INFO @ Sat, 11 Dec 2021 11:57:30: 2000000 INFO @ Sat, 11 Dec 2021 11:57:38: 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 11:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.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 11:57:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:57:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:57:47: 4000000 INFO @ Sat, 11 Dec 2021 11:57:51: 1000000 INFO @ Sat, 11 Dec 2021 11:57:55: 5000000 INFO @ Sat, 11 Dec 2021 11:58:02: 2000000 INFO @ Sat, 11 Dec 2021 11:58:04: 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 11:58:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.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 11:58:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:58:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:58:12: 3000000 INFO @ Sat, 11 Dec 2021 11:58:13: 7000000 INFO @ Sat, 11 Dec 2021 11:58:22: 8000000 INFO @ Sat, 11 Dec 2021 11:58:23: 1000000 INFO @ Sat, 11 Dec 2021 11:58:23: 4000000 INFO @ Sat, 11 Dec 2021 11:58:28: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:58:28: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:58:28: #1 total tags in treatment: 3934837 INFO @ Sat, 11 Dec 2021 11:58:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:58:28: #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 11:58:28: #1 tags after filtering in treatment: 3821480 INFO @ Sat, 11 Dec 2021 11:58:28: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:58:28: #1 finished! INFO @ Sat, 11 Dec 2021 11:58:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:58:28: #2 number of paired peaks: 1676 INFO @ Sat, 11 Dec 2021 11:58:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:58:28: start X-correlation... INFO @ Sat, 11 Dec 2021 11:58:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:58:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:58:28: #2 predicted fragment length is 204 bps INFO @ Sat, 11 Dec 2021 11:58:28: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 11 Dec 2021 11:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.05_model.r INFO @ Sat, 11 Dec 2021 11:58:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:58:33: 2000000 INFO @ Sat, 11 Dec 2021 11:58:34: 5000000 INFO @ Sat, 11 Dec 2021 11:58:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:58:43: 3000000 INFO @ Sat, 11 Dec 2021 11:58:44: 6000000 INFO @ Sat, 11 Dec 2021 11:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.05_summits.bed INFO @ Sat, 11 Dec 2021 11:58:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3079 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:58:54: 4000000 INFO @ Sat, 11 Dec 2021 11:58:55: 7000000 INFO @ Sat, 11 Dec 2021 11:59:04: 5000000 INFO @ Sat, 11 Dec 2021 11:59:06: 8000000 INFO @ Sat, 11 Dec 2021 11:59:12: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:59:12: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:59:12: #1 total tags in treatment: 3934837 INFO @ Sat, 11 Dec 2021 11:59:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:59:12: #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 11:59:12: #1 tags after filtering in treatment: 3821480 INFO @ Sat, 11 Dec 2021 11:59:12: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:59:12: #1 finished! INFO @ Sat, 11 Dec 2021 11:59:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:59:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:59:12: #2 number of paired peaks: 1676 INFO @ Sat, 11 Dec 2021 11:59:12: start model_add_line... INFO @ Sat, 11 Dec 2021 11:59:12: start X-correlation... INFO @ Sat, 11 Dec 2021 11:59:12: end of X-cor INFO @ Sat, 11 Dec 2021 11:59:12: #2 finished! INFO @ Sat, 11 Dec 2021 11:59:12: #2 predicted fragment length is 204 bps INFO @ Sat, 11 Dec 2021 11:59:12: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 11 Dec 2021 11:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.10_model.r INFO @ Sat, 11 Dec 2021 11:59:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:59:15: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:59:24: 7000000 INFO @ Sat, 11 Dec 2021 11:59:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:59:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:59:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:59:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.10_summits.bed INFO @ Sat, 11 Dec 2021 11:59:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1769 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:59:34: 8000000 INFO @ Sat, 11 Dec 2021 11:59:40: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:59:40: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:59:40: #1 total tags in treatment: 3934837 INFO @ Sat, 11 Dec 2021 11:59:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:59:40: #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 11:59:40: #1 tags after filtering in treatment: 3821480 INFO @ Sat, 11 Dec 2021 11:59:40: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:59:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:59:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:59:40: #2 number of paired peaks: 1676 INFO @ Sat, 11 Dec 2021 11:59:40: start model_add_line... INFO @ Sat, 11 Dec 2021 11:59:40: start X-correlation... INFO @ Sat, 11 Dec 2021 11:59:40: end of X-cor INFO @ Sat, 11 Dec 2021 11:59:40: #2 finished! INFO @ Sat, 11 Dec 2021 11:59:40: #2 predicted fragment length is 204 bps INFO @ Sat, 11 Dec 2021 11:59:40: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 11 Dec 2021 11:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.20_model.r INFO @ Sat, 11 Dec 2021 11:59:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:59:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:59:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:00:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:00:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:00:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005690/SRX9005690.20_summits.bed INFO @ Sat, 11 Dec 2021 12:00:00: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (803 records, 4 fields): 4 millis CompletedMACS2peakCalling