Job ID = 16436851 SRX = SRX8948329 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 60890 READS because READLEN < 1 Read 4514098 spots for SRR12453886/SRR12453886.sra Written 4514098 spots for SRR12453886/SRR12453886.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436979 ("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_rmdup_core] processing reference chr2L... [bam_rmdup_core] 3 unmatched pairs [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] 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] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 268118 / 4353248 = 0.0616 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.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 @ Tue, 02 Aug 2022 12:10:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:10:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:10:30: 1000000 INFO @ Tue, 02 Aug 2022 12:10:37: 2000000 INFO @ Tue, 02 Aug 2022 12:10:44: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:10:51: 4000000 INFO @ Tue, 02 Aug 2022 12:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.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 @ Tue, 02 Aug 2022 12:10:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:10:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:10:57: 5000000 INFO @ Tue, 02 Aug 2022 12:10:58: 1000000 INFO @ Tue, 02 Aug 2022 12:11:03: 2000000 INFO @ Tue, 02 Aug 2022 12:11:04: 6000000 INFO @ Tue, 02 Aug 2022 12:11:09: 3000000 INFO @ Tue, 02 Aug 2022 12:11:11: 7000000 INFO @ Tue, 02 Aug 2022 12:11:15: 4000000 INFO @ Tue, 02 Aug 2022 12:11:18: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:11:20: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:11:20: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:11:20: #1 total tags in treatment: 4063582 INFO @ Tue, 02 Aug 2022 12:11:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:11:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:11:20: #1 tags after filtering in treatment: 3837398 INFO @ Tue, 02 Aug 2022 12:11:20: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 12:11:20: #1 finished! INFO @ Tue, 02 Aug 2022 12:11:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:11:20: #2 number of paired peaks: 9 WARNING @ Tue, 02 Aug 2022 12:11:20: Too few paired peaks (9) 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 @ Tue, 02 Aug 2022 12:11:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.05_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/SRX8948329/SRX8948329.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:11:21: 5000000 INFO @ Tue, 02 Aug 2022 12:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.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 @ Tue, 02 Aug 2022 12:11:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:11:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:11:26: 6000000 INFO @ Tue, 02 Aug 2022 12:11:30: 1000000 INFO @ Tue, 02 Aug 2022 12:11:32: 7000000 INFO @ Tue, 02 Aug 2022 12:11:37: 8000000 INFO @ Tue, 02 Aug 2022 12:11:38: 2000000 INFO @ Tue, 02 Aug 2022 12:11:39: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:11:39: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:11:39: #1 total tags in treatment: 4063582 INFO @ Tue, 02 Aug 2022 12:11:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:11:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:11:39: #1 tags after filtering in treatment: 3837398 INFO @ Tue, 02 Aug 2022 12:11:39: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 12:11:39: #1 finished! INFO @ Tue, 02 Aug 2022 12:11:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:11:39: #2 number of paired peaks: 9 WARNING @ Tue, 02 Aug 2022 12:11:39: Too few paired peaks (9) 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 @ Tue, 02 Aug 2022 12:11:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.10_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/SRX8948329/SRX8948329.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:11:46: 3000000 INFO @ Tue, 02 Aug 2022 12:11:54: 4000000 INFO @ Tue, 02 Aug 2022 12:12:02: 5000000 INFO @ Tue, 02 Aug 2022 12:12:10: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:12:18: 7000000 INFO @ Tue, 02 Aug 2022 12:12:25: 8000000 INFO @ Tue, 02 Aug 2022 12:12:27: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:12:27: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:12:27: #1 total tags in treatment: 4063582 INFO @ Tue, 02 Aug 2022 12:12:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:12:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:12:27: #1 tags after filtering in treatment: 3837398 INFO @ Tue, 02 Aug 2022 12:12:27: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 12:12:27: #1 finished! INFO @ Tue, 02 Aug 2022 12:12:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:12:27: #2 number of paired peaks: 9 WARNING @ Tue, 02 Aug 2022 12:12:27: Too few paired peaks (9) 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 @ Tue, 02 Aug 2022 12:12:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX8948329/SRX8948329.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。