Job ID = 5791176 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:52:48 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 : 7,888,427 reads read : 15,776,854 reads written : 15,776,854 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: 00:09:04 7888427 reads; of these: 7888427 (100.00%) were paired; of these: 5944593 (75.36%) aligned concordantly 0 times 1604601 (20.34%) aligned concordantly exactly 1 time 339233 (4.30%) aligned concordantly >1 times ---- 5944593 pairs aligned concordantly 0 times; of these: 2673694 (44.98%) aligned discordantly 1 time ---- 3270899 pairs aligned 0 times concordantly or discordantly; of these: 6541798 mates make up the pairs; of these: 5437410 (83.12%) aligned 0 times 224142 (3.43%) aligned exactly 1 time 880246 (13.46%) aligned >1 times 65.54% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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] 739512 / 4477581 = 0.1652 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 09:12:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.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 09:12:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:12:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:12:55: 1000000 INFO @ Wed, 22 Apr 2020 09:13:04: 2000000 INFO @ Wed, 22 Apr 2020 09:13:12: 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 @ Wed, 22 Apr 2020 09:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.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 09:13:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:13:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:13:22: 4000000 INFO @ Wed, 22 Apr 2020 09:13:25: 1000000 INFO @ Wed, 22 Apr 2020 09:13:31: 5000000 INFO @ Wed, 22 Apr 2020 09:13:35: 2000000 INFO @ Wed, 22 Apr 2020 09:13:40: 6000000 INFO @ Wed, 22 Apr 2020 09:13:44: 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 @ Wed, 22 Apr 2020 09:13:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.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 09:13:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:13:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:13:50: 7000000 INFO @ Wed, 22 Apr 2020 09:13:54: 4000000 INFO @ Wed, 22 Apr 2020 09:13:58: 1000000 INFO @ Wed, 22 Apr 2020 09:14:00: 8000000 INFO @ Wed, 22 Apr 2020 09:14:04: 5000000 INFO @ Wed, 22 Apr 2020 09:14:09: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:14:09: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:14:09: #1 total tags in treatment: 1603616 INFO @ Wed, 22 Apr 2020 09:14:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:14:09: #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 09:14:09: #1 tags after filtering in treatment: 1285495 INFO @ Wed, 22 Apr 2020 09:14:09: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:14:09: #1 finished! INFO @ Wed, 22 Apr 2020 09:14:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:14:09: #2 number of paired peaks: 13 WARNING @ Wed, 22 Apr 2020 09:14:09: Too few paired peaks (13) 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 09:14:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.05_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/SRX6614968/SRX6614968.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:14:09: 2000000 INFO @ Wed, 22 Apr 2020 09:14:15: 6000000 INFO @ Wed, 22 Apr 2020 09:14:21: 3000000 INFO @ Wed, 22 Apr 2020 09:14:25: 7000000 INFO @ Wed, 22 Apr 2020 09:14:33: 4000000 INFO @ Wed, 22 Apr 2020 09:14:35: 8000000 INFO @ Wed, 22 Apr 2020 09:14:44: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:14:44: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:14:44: #1 total tags in treatment: 1603616 INFO @ Wed, 22 Apr 2020 09:14:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:14:44: #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 09:14:44: #1 tags after filtering in treatment: 1285495 INFO @ Wed, 22 Apr 2020 09:14:44: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:14:44: #1 finished! INFO @ Wed, 22 Apr 2020 09:14:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:14:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:14:44: #2 number of paired peaks: 13 WARNING @ Wed, 22 Apr 2020 09:14:44: Too few paired peaks (13) 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 09:14:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.10_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/SRX6614968/SRX6614968.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:14:45: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:14:56: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:15:06: 7000000 INFO @ Wed, 22 Apr 2020 09:15:17: 8000000 INFO @ Wed, 22 Apr 2020 09:15:26: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:15:26: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:15:26: #1 total tags in treatment: 1603616 INFO @ Wed, 22 Apr 2020 09:15:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:15:26: #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 09:15:26: #1 tags after filtering in treatment: 1285495 INFO @ Wed, 22 Apr 2020 09:15:26: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:15:26: #1 finished! INFO @ Wed, 22 Apr 2020 09:15:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:15:26: #2 number of paired peaks: 13 WARNING @ Wed, 22 Apr 2020 09:15:26: Too few paired peaks (13) 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 09:15:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.20_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/sacCer3/SRX6614968/SRX6614968.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614968/SRX6614968.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling