Job ID = 14171271 SRX = SRX9005657 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1138861 READS because READLEN < 1 Read 12874535 spots for SRR12515058/SRR12515058.sra Written 12874535 spots for SRR12515058/SRR12515058.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171863 ("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] 1 unmatched pairs [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] 2 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 1 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] 1 unmatched pairs [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] 4 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1829193 / 10751328 = 0.1701 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 11:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.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 11:47:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:47:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:47:24: 1000000 INFO @ Sat, 11 Dec 2021 11:47:37: 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 @ Sat, 11 Dec 2021 11:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.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 11:47:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:47:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:47:51: 3000000 INFO @ Sat, 11 Dec 2021 11:47:54: 1000000 INFO @ Sat, 11 Dec 2021 11:48:05: 4000000 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 11:48:09: 2000000 INFO @ Sat, 11 Dec 2021 11:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.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 11:48:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:48:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:48:20: 5000000 INFO @ Sat, 11 Dec 2021 11:48:24: 1000000 INFO @ Sat, 11 Dec 2021 11:48:24: 3000000 INFO @ Sat, 11 Dec 2021 11:48:35: 6000000 INFO @ Sat, 11 Dec 2021 11:48:38: 2000000 INFO @ Sat, 11 Dec 2021 11:48:39: 4000000 INFO @ Sat, 11 Dec 2021 11:48:50: 7000000 INFO @ Sat, 11 Dec 2021 11:48:53: 3000000 INFO @ Sat, 11 Dec 2021 11:48:54: 5000000 INFO @ Sat, 11 Dec 2021 11:49:05: 8000000 INFO @ Sat, 11 Dec 2021 11:49:08: 4000000 INFO @ Sat, 11 Dec 2021 11:49:09: 6000000 INFO @ Sat, 11 Dec 2021 11:49:21: 9000000 INFO @ Sat, 11 Dec 2021 11:49:22: 5000000 INFO @ Sat, 11 Dec 2021 11:49:24: 7000000 INFO @ Sat, 11 Dec 2021 11:49:36: 6000000 INFO @ Sat, 11 Dec 2021 11:49:37: 10000000 INFO @ Sat, 11 Dec 2021 11:49:40: 8000000 INFO @ Sat, 11 Dec 2021 11:49:50: 7000000 INFO @ Sat, 11 Dec 2021 11:49:53: 11000000 INFO @ Sat, 11 Dec 2021 11:49:57: 9000000 INFO @ Sat, 11 Dec 2021 11:50:05: 8000000 INFO @ Sat, 11 Dec 2021 11:50:09: 12000000 INFO @ Sat, 11 Dec 2021 11:50:13: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:50:20: 9000000 INFO @ Sat, 11 Dec 2021 11:50:26: 13000000 INFO @ Sat, 11 Dec 2021 11:50:30: 11000000 INFO @ Sat, 11 Dec 2021 11:50:35: 10000000 INFO @ Sat, 11 Dec 2021 11:50:43: 14000000 INFO @ Sat, 11 Dec 2021 11:50:46: 12000000 INFO @ Sat, 11 Dec 2021 11:50:53: 11000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:50:59: 15000000 INFO @ Sat, 11 Dec 2021 11:51:02: 13000000 INFO @ Sat, 11 Dec 2021 11:51:09: 12000000 INFO @ Sat, 11 Dec 2021 11:51:16: 16000000 INFO @ Sat, 11 Dec 2021 11:51:19: 14000000 INFO @ Sat, 11 Dec 2021 11:51:24: 13000000 INFO @ Sat, 11 Dec 2021 11:51:33: 17000000 INFO @ Sat, 11 Dec 2021 11:51:36: 15000000 INFO @ Sat, 11 Dec 2021 11:51:39: 14000000 INFO @ Sat, 11 Dec 2021 11:51:49: 18000000 INFO @ Sat, 11 Dec 2021 11:51:52: 16000000 INFO @ Sat, 11 Dec 2021 11:51:53: 15000000 INFO @ Sat, 11 Dec 2021 11:52:05: 19000000 INFO @ Sat, 11 Dec 2021 11:52:07: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:52:07: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:52:07: #1 total tags in treatment: 8740276 INFO @ Sat, 11 Dec 2021 11:52:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:07: #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 11:52:08: #1 tags after filtering in treatment: 7212862 INFO @ Sat, 11 Dec 2021 11:52:08: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 11:52:08: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:08: 16000000 INFO @ Sat, 11 Dec 2021 11:52:09: #2 number of paired peaks: 6365 INFO @ Sat, 11 Dec 2021 11:52:09: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:09: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:09: 17000000 INFO @ Sat, 11 Dec 2021 11:52:09: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:09: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:09: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 11:52:09: #2 alternative fragment length(s) may be 225 bps INFO @ Sat, 11 Dec 2021 11:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.05_model.r WARNING @ Sat, 11 Dec 2021 11:52:09: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:09: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Sat, 11 Dec 2021 11:52:09: #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 11:52:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:22: 17000000 INFO @ Sat, 11 Dec 2021 11:52:24: 18000000 INFO @ Sat, 11 Dec 2021 11:52:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:52:37: 18000000 INFO @ Sat, 11 Dec 2021 11:52:38: 19000000 INFO @ Sat, 11 Dec 2021 11:52:40: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:52:40: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:52:40: #1 total tags in treatment: 8740276 INFO @ Sat, 11 Dec 2021 11:52:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:40: #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 11:52:41: #1 tags after filtering in treatment: 7212862 INFO @ Sat, 11 Dec 2021 11:52:41: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 11:52:41: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:42: #2 number of paired peaks: 6365 INFO @ Sat, 11 Dec 2021 11:52:42: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:42: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:42: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:42: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:42: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 11:52:42: #2 alternative fragment length(s) may be 225 bps INFO @ Sat, 11 Dec 2021 11:52:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.10_model.r WARNING @ Sat, 11 Dec 2021 11:52:42: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:42: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Sat, 11 Dec 2021 11:52:42: #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 11:52:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.05_summits.bed INFO @ Sat, 11 Dec 2021 11:52:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9254 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:52:51: 19000000 INFO @ Sat, 11 Dec 2021 11:52:53: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:52:53: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:52:53: #1 total tags in treatment: 8740276 INFO @ Sat, 11 Dec 2021 11:52:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:53: #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 11:52:53: #1 tags after filtering in treatment: 7212862 INFO @ Sat, 11 Dec 2021 11:52:53: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 11:52:53: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:54: #2 number of paired peaks: 6365 INFO @ Sat, 11 Dec 2021 11:52:54: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:54: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:54: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:54: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:54: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 11:52:54: #2 alternative fragment length(s) may be 225 bps INFO @ Sat, 11 Dec 2021 11:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.20_model.r WARNING @ Sat, 11 Dec 2021 11:52:54: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:54: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Sat, 11 Dec 2021 11:52:54: #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 11:52:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.10_summits.bed INFO @ Sat, 11 Dec 2021 11:53:17: Done! pass1 - making usageList (15 chroms): 12 millis pass2 - checking and writing primary data (7563 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:53:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005657/SRX9005657.20_summits.bed INFO @ Sat, 11 Dec 2021 11:53:30: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5499 records, 4 fields): 18 millis CompletedMACS2peakCalling