Job ID = 5791179 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:47:32 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-21T23:47:32 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 6,581,097 reads read : 13,162,194 reads written : 13,162,194 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:07:25 6581097 reads; of these: 6581097 (100.00%) were paired; of these: 4182396 (63.55%) aligned concordantly 0 times 2003583 (30.44%) aligned concordantly exactly 1 time 395118 (6.00%) aligned concordantly >1 times ---- 4182396 pairs aligned concordantly 0 times; of these: 1552884 (37.13%) aligned discordantly 1 time ---- 2629512 pairs aligned 0 times concordantly or discordantly; of these: 5259024 mates make up the pairs; of these: 4570624 (86.91%) aligned 0 times 144574 (2.75%) aligned exactly 1 time 543826 (10.34%) aligned >1 times 65.27% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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_sort_core] merging from 8 files... [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] 635840 / 3845378 = 0.1654 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 @ Wed, 22 Apr 2020 09:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.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 @ Wed, 22 Apr 2020 09:07:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:07:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:07:59: 1000000 INFO @ Wed, 22 Apr 2020 09:08:10: 2000000 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 @ Wed, 22 Apr 2020 09:08:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.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 @ Wed, 22 Apr 2020 09:08:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:08:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:08:21: 3000000 INFO @ Wed, 22 Apr 2020 09:08:31: 1000000 INFO @ Wed, 22 Apr 2020 09:08:33: 4000000 INFO @ Wed, 22 Apr 2020 09:08:43: 2000000 INFO @ Wed, 22 Apr 2020 09:08:46: 5000000 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 @ Wed, 22 Apr 2020 09:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.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 @ Wed, 22 Apr 2020 09:08:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:08:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:08:55: 3000000 INFO @ Wed, 22 Apr 2020 09:08:58: 6000000 INFO @ Wed, 22 Apr 2020 09:09:01: 1000000 INFO @ Wed, 22 Apr 2020 09:09:07: 4000000 INFO @ Wed, 22 Apr 2020 09:09:09: 7000000 INFO @ Wed, 22 Apr 2020 09:09:13: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:09:13: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:09:13: #1 total tags in treatment: 1963973 INFO @ Wed, 22 Apr 2020 09:09:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:09:13: #1 tags after filtering in treatment: 1558476 INFO @ Wed, 22 Apr 2020 09:09:13: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 09:09:13: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:13: 2000000 INFO @ Wed, 22 Apr 2020 09:09:13: #2 number of paired peaks: 17 WARNING @ Wed, 22 Apr 2020 09:09:13: Too few paired peaks (17) 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 @ Wed, 22 Apr 2020 09:09:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.05_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/SRX6614971/SRX6614971.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:09:19: 5000000 INFO @ Wed, 22 Apr 2020 09:09:25: 3000000 INFO @ Wed, 22 Apr 2020 09:09:32: 6000000 INFO @ Wed, 22 Apr 2020 09:09:38: 4000000 INFO @ Wed, 22 Apr 2020 09:09:43: 7000000 INFO @ Wed, 22 Apr 2020 09:09:46: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:09:46: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:09:46: #1 total tags in treatment: 1963973 INFO @ Wed, 22 Apr 2020 09:09:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:09:46: #1 tags after filtering in treatment: 1558476 INFO @ Wed, 22 Apr 2020 09:09:46: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 09:09:46: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:46: #2 number of paired peaks: 17 WARNING @ Wed, 22 Apr 2020 09:09:46: Too few paired peaks (17) 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 @ Wed, 22 Apr 2020 09:09:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.10_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/SRX6614971/SRX6614971.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:09:49: 5000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:10:01: 6000000 INFO @ Wed, 22 Apr 2020 09:10:11: 7000000 INFO @ Wed, 22 Apr 2020 09:10:14: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:10:14: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:10:14: #1 total tags in treatment: 1963973 INFO @ Wed, 22 Apr 2020 09:10:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:10:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:10:14: #1 tags after filtering in treatment: 1558476 INFO @ Wed, 22 Apr 2020 09:10:14: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 09:10:14: #1 finished! INFO @ Wed, 22 Apr 2020 09:10:14: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:10:14: #2 number of paired peaks: 17 WARNING @ Wed, 22 Apr 2020 09:10:14: Too few paired peaks (17) 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 @ Wed, 22 Apr 2020 09:10:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.20_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/SRX6614971/SRX6614971.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614971/SRX6614971.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling