Job ID = 10223897 SRX = ERX4439638 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-10-15T23:41:11 prefetch.2.10.7: 1) Downloading 'ERR4501567'... 2020-10-15T23:41:11 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:41:50 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:41:51 prefetch.2.10.7: 'ERR4501567' is valid 2020-10-15T23:41:51 prefetch.2.10.7: 1) 'ERR4501567' was downloaded successfully 2020-10-15T23:42:18 prefetch.2.10.7: 'ERR4501567' has 5 unresolved dependencies 2020-10-15T23:42:18 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_001136.8?vdb-ctx=refseq'... 2020-10-15T23:42:18 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:42:30 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:42:30 prefetch.2.10.7: 2) 'ncbi-acc:NC_001136.8?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:42:30 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_001139.7?vdb-ctx=refseq'... 2020-10-15T23:42:30 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:42:39 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:42:39 prefetch.2.10.7: 3) 'ncbi-acc:NC_001139.7?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:42:39 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NC_001144.4?vdb-ctx=refseq'... 2020-10-15T23:42:39 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:42:51 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:42:51 prefetch.2.10.7: 4) 'ncbi-acc:NC_001144.4?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:42:51 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NC_001147.5?vdb-ctx=refseq'... 2020-10-15T23:42:51 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:42:59 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:42:59 prefetch.2.10.7: 5) 'ncbi-acc:NC_001147.5?vdb-ctx=refseq' was downloaded successfully 2020-10-15T23:42:59 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NC_001224.1?vdb-ctx=refseq'... 2020-10-15T23:42:59 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T23:43:09 prefetch.2.10.7: HTTPS download succeed 2020-10-15T23:43:09 prefetch.2.10.7: 6) 'ncbi-acc:NC_001224.1?vdb-ctx=refseq' was downloaded successfully Read 3446098 spots for ERR4501567/ERR4501567.sra Written 3446098 spots for ERR4501567/ERR4501567.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: 00:02:34 3446098 reads; of these: 3446098 (100.00%) were paired; of these: 921858 (26.75%) aligned concordantly 0 times 2198217 (63.79%) aligned concordantly exactly 1 time 326023 (9.46%) aligned concordantly >1 times ---- 921858 pairs aligned concordantly 0 times; of these: 428094 (46.44%) aligned discordantly 1 time ---- 493764 pairs aligned 0 times concordantly or discordantly; of these: 987528 mates make up the pairs; of these: 793419 (80.34%) aligned 0 times 60041 (6.08%) aligned exactly 1 time 134068 (13.58%) aligned >1 times 88.49% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 42503 / 2923323 = 0.0145 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 08:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.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 08:49:20: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:49:20: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:49:26: 1000000 INFO @ Fri, 16 Oct 2020 08:49:32: 2000000 INFO @ Fri, 16 Oct 2020 08:49:38: 3000000 INFO @ Fri, 16 Oct 2020 08:49:44: 4000000 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 08:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.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 08:49:50: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:49:50: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:49:51: 5000000 INFO @ Fri, 16 Oct 2020 08:49:58: 6000000 INFO @ Fri, 16 Oct 2020 08:49:58: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:49:58: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:49:58: #1 total tags in treatment: 2488482 INFO @ Fri, 16 Oct 2020 08:49:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:49:58: #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 08:49:58: #1 tags after filtering in treatment: 2215571 INFO @ Fri, 16 Oct 2020 08:49:58: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:49:58: #1 finished! INFO @ Fri, 16 Oct 2020 08:49:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:49:58: #2 number of paired peaks: 88 WARNING @ Fri, 16 Oct 2020 08:49:58: Too few paired peaks (88) 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 08:49:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.05_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/ERX4439638/ERX4439638.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:49:59: 1000000 INFO @ Fri, 16 Oct 2020 08:50:06: 2000000 INFO @ Fri, 16 Oct 2020 08:50:13: 3000000 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 08:50:19: 4000000 INFO @ Fri, 16 Oct 2020 08:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.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 08:50:21: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:50:21: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:50:27: 5000000 INFO @ Fri, 16 Oct 2020 08:50:28: 1000000 INFO @ Fri, 16 Oct 2020 08:50:35: 6000000 INFO @ Fri, 16 Oct 2020 08:50:35: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:50:35: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:50:35: #1 total tags in treatment: 2488482 INFO @ Fri, 16 Oct 2020 08:50:35: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:50:35: #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 08:50:35: #1 tags after filtering in treatment: 2215571 INFO @ Fri, 16 Oct 2020 08:50:35: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:50:35: #1 finished! INFO @ Fri, 16 Oct 2020 08:50:35: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:50:36: #2 number of paired peaks: 88 WARNING @ Fri, 16 Oct 2020 08:50:36: Too few paired peaks (88) 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 08:50:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.10_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/sacCer3/ERX4439638/ERX4439638.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:50:36: 2000000 INFO @ Fri, 16 Oct 2020 08:50:43: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:50:50: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:50:57: 5000000 INFO @ Fri, 16 Oct 2020 08:51:03: 6000000 INFO @ Fri, 16 Oct 2020 08:51:03: #1 tag size is determined as 100 bps INFO @ Fri, 16 Oct 2020 08:51:03: #1 tag size = 100 INFO @ Fri, 16 Oct 2020 08:51:03: #1 total tags in treatment: 2488482 INFO @ Fri, 16 Oct 2020 08:51:03: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:51:03: #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 08:51:03: #1 tags after filtering in treatment: 2215571 INFO @ Fri, 16 Oct 2020 08:51:03: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 08:51:03: #1 finished! INFO @ Fri, 16 Oct 2020 08:51:03: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:51:04: #2 number of paired peaks: 88 WARNING @ Fri, 16 Oct 2020 08:51:04: Too few paired peaks (88) 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 08:51:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.20_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/ERX4439638/ERX4439638.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX4439638/ERX4439638.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling