Job ID = 14167174 SRX = SRX10340474 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1178025 READS because READLEN < 1 Read 14005004 spots for SRR13962483/SRR13962483.sra Written 14005004 spots for SRR13962483/SRR13962483.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167765 ("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] 4 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 4 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 3 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 6 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] 2 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] 2103692 / 11659228 = 0.1804 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 @ Fri, 10 Dec 2021 11:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.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 @ Fri, 10 Dec 2021 11:19:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:19:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:19:15: 1000000 INFO @ Fri, 10 Dec 2021 11:19:22: 2000000 INFO @ Fri, 10 Dec 2021 11:19:29: 3000000 INFO @ Fri, 10 Dec 2021 11:19:35: 4000000 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 @ Fri, 10 Dec 2021 11:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.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 @ Fri, 10 Dec 2021 11:19:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:19:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:19:43: 5000000 INFO @ Fri, 10 Dec 2021 11:19:48: 1000000 INFO @ Fri, 10 Dec 2021 11:19:52: 6000000 INFO @ Fri, 10 Dec 2021 11:19:58: 2000000 INFO @ Fri, 10 Dec 2021 11:20:00: 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 @ Fri, 10 Dec 2021 11:20:07: 3000000 INFO @ Fri, 10 Dec 2021 11:20:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.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 @ Fri, 10 Dec 2021 11:20:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:20:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:20:09: 8000000 INFO @ Fri, 10 Dec 2021 11:20:17: 4000000 INFO @ Fri, 10 Dec 2021 11:20:18: 9000000 INFO @ Fri, 10 Dec 2021 11:20:18: 1000000 INFO @ Fri, 10 Dec 2021 11:20:26: 10000000 INFO @ Fri, 10 Dec 2021 11:20:27: 5000000 INFO @ Fri, 10 Dec 2021 11:20:28: 2000000 INFO @ Fri, 10 Dec 2021 11:20:35: 11000000 INFO @ Fri, 10 Dec 2021 11:20:37: 6000000 INFO @ Fri, 10 Dec 2021 11:20:38: 3000000 INFO @ Fri, 10 Dec 2021 11:20:44: 12000000 INFO @ Fri, 10 Dec 2021 11:20:46: 7000000 INFO @ Fri, 10 Dec 2021 11:20:47: 4000000 INFO @ Fri, 10 Dec 2021 11:20:52: 13000000 INFO @ Fri, 10 Dec 2021 11:20:56: 8000000 INFO @ Fri, 10 Dec 2021 11:20:57: 5000000 INFO @ Fri, 10 Dec 2021 11:21:01: 14000000 INFO @ Fri, 10 Dec 2021 11:21:06: 9000000 INFO @ Fri, 10 Dec 2021 11:21:07: 6000000 INFO @ Fri, 10 Dec 2021 11:21:10: 15000000 INFO @ Fri, 10 Dec 2021 11:21:16: 10000000 INFO @ Fri, 10 Dec 2021 11:21:17: 7000000 INFO @ Fri, 10 Dec 2021 11:21:19: 16000000 INFO @ Fri, 10 Dec 2021 11:21:25: 11000000 INFO @ Fri, 10 Dec 2021 11:21:26: 8000000 INFO @ Fri, 10 Dec 2021 11:21:28: 17000000 INFO @ Fri, 10 Dec 2021 11:21:35: 12000000 INFO @ Fri, 10 Dec 2021 11:21:36: 9000000 INFO @ Fri, 10 Dec 2021 11:21:36: 18000000 INFO @ Fri, 10 Dec 2021 11:21:45: 13000000 INFO @ Fri, 10 Dec 2021 11:21:45: 19000000 INFO @ Fri, 10 Dec 2021 11:21:46: 10000000 INFO @ Fri, 10 Dec 2021 11:21:55: 14000000 INFO @ Fri, 10 Dec 2021 11:21:55: 20000000 INFO @ Fri, 10 Dec 2021 11:21:56: 11000000 INFO @ Fri, 10 Dec 2021 11:21:59: #1 tag size is determined as 123 bps INFO @ Fri, 10 Dec 2021 11:21:59: #1 tag size = 123 INFO @ Fri, 10 Dec 2021 11:21:59: #1 total tags in treatment: 9131494 INFO @ Fri, 10 Dec 2021 11:21:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:21:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:21:59: #1 tags after filtering in treatment: 8755132 INFO @ Fri, 10 Dec 2021 11:21:59: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:21:59: #1 finished! INFO @ Fri, 10 Dec 2021 11:21:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:21:59: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:22:00: #2 number of paired peaks: 60 WARNING @ Fri, 10 Dec 2021 11:22:00: Too few paired peaks (60) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 10 Dec 2021 11:22:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:22:04: 15000000 INFO @ Fri, 10 Dec 2021 11:22:05: 12000000 INFO @ Fri, 10 Dec 2021 11:22:13: 16000000 INFO @ Fri, 10 Dec 2021 11:22:14: 13000000 INFO @ Fri, 10 Dec 2021 11:22:22: 17000000 INFO @ Fri, 10 Dec 2021 11:22:23: 14000000 INFO @ Fri, 10 Dec 2021 11:22:31: 18000000 INFO @ Fri, 10 Dec 2021 11:22:32: 15000000 INFO @ Fri, 10 Dec 2021 11:22:40: 19000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:22:41: 16000000 INFO @ Fri, 10 Dec 2021 11:22:49: 20000000 INFO @ Fri, 10 Dec 2021 11:22:50: 17000000 INFO @ Fri, 10 Dec 2021 11:22:53: #1 tag size is determined as 123 bps INFO @ Fri, 10 Dec 2021 11:22:53: #1 tag size = 123 INFO @ Fri, 10 Dec 2021 11:22:53: #1 total tags in treatment: 9131494 INFO @ Fri, 10 Dec 2021 11:22:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:22:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:22:53: #1 tags after filtering in treatment: 8755132 INFO @ Fri, 10 Dec 2021 11:22:53: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:22:53: #1 finished! INFO @ Fri, 10 Dec 2021 11:22:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:22:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:22:54: #2 number of paired peaks: 60 WARNING @ Fri, 10 Dec 2021 11:22:54: Too few paired peaks (60) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 10 Dec 2021 11:22:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:22:58: 18000000 INFO @ Fri, 10 Dec 2021 11:23:07: 19000000 INFO @ Fri, 10 Dec 2021 11:23:16: 20000000 INFO @ Fri, 10 Dec 2021 11:23:21: #1 tag size is determined as 123 bps INFO @ Fri, 10 Dec 2021 11:23:21: #1 tag size = 123 INFO @ Fri, 10 Dec 2021 11:23:21: #1 total tags in treatment: 9131494 INFO @ Fri, 10 Dec 2021 11:23:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:23:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:23:21: #1 tags after filtering in treatment: 8755132 INFO @ Fri, 10 Dec 2021 11:23:21: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 10 Dec 2021 11:23:21: #1 finished! INFO @ Fri, 10 Dec 2021 11:23:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:23:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:23:21: #2 number of paired peaks: 60 WARNING @ Fri, 10 Dec 2021 11:23:21: Too few paired peaks (60) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 10 Dec 2021 11:23:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX10340474/SRX10340474.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling