Job ID = 10223805 SRX = ERX4439569 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:08:41 prefetch.2.10.7: 1) Downloading 'ERR4501498'... 2020-10-15T23:08:41 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:09:21 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:09:21 prefetch.2.10.7: 'ERR4501498' is valid 2020-10-15T23:09:21 prefetch.2.10.7: 1) 'ERR4501498' was downloaded successfully 2020-10-15T23:09:49 prefetch.2.10.7: 'ERR4501498' has 5 unresolved dependencies 2020-10-15T23:09:49 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:09:49 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:10:01 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:10:01 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:10:01 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:10:01 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:10:13 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:10:13 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:10:13 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:10:13 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:10:21 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:10:21 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:10:21 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:10:21 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:10:32 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:10:32 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:10:32 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:10:32 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:10:42 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:10:42 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 4158437 spots for ERR4501498/ERR4501498.sra Written 4158437 spots for ERR4501498/ERR4501498.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:07 4158437 reads; of these: 4158437 (100.00%) were paired; of these: 1074796 (25.85%) aligned concordantly 0 times 2735784 (65.79%) aligned concordantly exactly 1 time 347857 (8.37%) aligned concordantly >1 times ---- 1074796 pairs aligned concordantly 0 times; of these: 444971 (41.40%) aligned discordantly 1 time ---- 629825 pairs aligned 0 times concordantly or discordantly; of these: 1259650 mates make up the pairs; of these: 1082224 (85.91%) aligned 0 times 63142 (5.01%) aligned exactly 1 time 114284 (9.07%) aligned >1 times 86.99% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 59143 / 3497854 = 0.0169 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 16 Oct 2020 08:18:02: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:18:02: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:18:10: 1000000 INFO @ Fri, 16 Oct 2020 08:18:17: 2000000 INFO @ Fri, 16 Oct 2020 08:18:24: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:18:32: 4000000 INFO @ Fri, 16 Oct 2020 08:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 16 Oct 2020 08:18:32: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:18:32: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:18:41: 5000000 INFO @ Fri, 16 Oct 2020 08:18:42: 1000000 INFO @ Fri, 16 Oct 2020 08:18:50: 6000000 INFO @ Fri, 16 Oct 2020 08:18:52: 2000000 INFO @ Fri, 16 Oct 2020 08:18:59: 7000000 INFO @ Fri, 16 Oct 2020 08:19:00: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:19:00: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:19:00: #1 total tags in treatment: 3033487 INFO @ Fri, 16 Oct 2020 08:19:00: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:19:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:19:00: #1 tags after filtering in treatment: 2686031 INFO @ Fri, 16 Oct 2020 08:19:00: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:19:00: #1 finished! INFO @ Fri, 16 Oct 2020 08:19:00: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:19:00: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 08:19:00: #2 number of paired peaks: 85 WARNING @ Fri, 16 Oct 2020 08:19:00: Too few paired peaks (85) 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, 16 Oct 2020 08:19:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.05_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/sacCer3/ERX4439569/ERX4439569.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:19:01: 3000000 INFO @ Fri, 16 Oct 2020 08:19:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 16 Oct 2020 08:19:02: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:19:02: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:19:11: 4000000 INFO @ Fri, 16 Oct 2020 08:19:12: 1000000 INFO @ Fri, 16 Oct 2020 08:19:21: 5000000 INFO @ Fri, 16 Oct 2020 08:19:23: 2000000 INFO @ Fri, 16 Oct 2020 08:19:31: 6000000 INFO @ Fri, 16 Oct 2020 08:19:33: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:19:40: 7000000 INFO @ Fri, 16 Oct 2020 08:19:41: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:19:41: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:19:41: #1 total tags in treatment: 3033487 INFO @ Fri, 16 Oct 2020 08:19:41: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:19:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:19:41: #1 tags after filtering in treatment: 2686031 INFO @ Fri, 16 Oct 2020 08:19:41: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:19:41: #1 finished! INFO @ Fri, 16 Oct 2020 08:19:41: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:19:41: #2 number of paired peaks: 85 WARNING @ Fri, 16 Oct 2020 08:19:41: Too few paired peaks (85) 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, 16 Oct 2020 08:19:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.10_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/sacCer3/ERX4439569/ERX4439569.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:19:42: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:19:51: 5000000 INFO @ Fri, 16 Oct 2020 08:20:00: 6000000 INFO @ Fri, 16 Oct 2020 08:20:09: 7000000 INFO @ Fri, 16 Oct 2020 08:20:10: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:20:10: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:20:10: #1 total tags in treatment: 3033487 INFO @ Fri, 16 Oct 2020 08:20:10: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:20:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 08:20:10: #1 tags after filtering in treatment: 2686031 INFO @ Fri, 16 Oct 2020 08:20:10: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:20:10: #1 finished! INFO @ Fri, 16 Oct 2020 08:20:10: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:20:10: #2 number of paired peaks: 85 WARNING @ Fri, 16 Oct 2020 08:20:10: Too few paired peaks (85) 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, 16 Oct 2020 08:20:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.20_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/sacCer3/ERX4439569/ERX4439569.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439569/ERX4439569.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling