Job ID = 5791169 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:43:28 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 ) 2020-04-21T23:54:45 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 ) 2020-04-21T23:54:45 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 : 6,621,015 reads read : 13,242,030 reads written : 13,242,030 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: 00:07:13 6621015 reads; of these: 6621015 (100.00%) were paired; of these: 4755087 (71.82%) aligned concordantly 0 times 1407872 (21.26%) aligned concordantly exactly 1 time 458056 (6.92%) aligned concordantly >1 times ---- 4755087 pairs aligned concordantly 0 times; of these: 1551977 (32.64%) aligned discordantly 1 time ---- 3203110 pairs aligned 0 times concordantly or discordantly; of these: 6406220 mates make up the pairs; of these: 5347430 (83.47%) aligned 0 times 155701 (2.43%) aligned exactly 1 time 903089 (14.10%) aligned >1 times 59.62% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 606800 / 3322401 = 0.1826 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 09:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.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 09:08:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:08:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:08:25: 1000000 INFO @ Wed, 22 Apr 2020 09:08:33: 2000000 INFO @ Wed, 22 Apr 2020 09:08:41: 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 09:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.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 09:08:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:08:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:08:49: 4000000 INFO @ Wed, 22 Apr 2020 09:08:55: 1000000 INFO @ Wed, 22 Apr 2020 09:08:58: 5000000 INFO @ Wed, 22 Apr 2020 09:09:04: 2000000 INFO @ Wed, 22 Apr 2020 09:09:07: 6000000 INFO @ Wed, 22 Apr 2020 09:09:12: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:09:12: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:09:12: #1 total tags in treatment: 1468533 INFO @ Wed, 22 Apr 2020 09:09:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:12: #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 09:09:12: #1 tags after filtering in treatment: 1179868 INFO @ Wed, 22 Apr 2020 09:09:12: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:09:12: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:13: #2 number of paired peaks: 32 WARNING @ Wed, 22 Apr 2020 09:09:13: Too few paired peaks (32) 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/SRX6614962/SRX6614962.05_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/SRX6614962/SRX6614962.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:09:13: 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 @ Wed, 22 Apr 2020 09:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.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 09:09:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:09:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:09:22: 4000000 INFO @ Wed, 22 Apr 2020 09:09:25: 1000000 INFO @ Wed, 22 Apr 2020 09:09:31: 5000000 INFO @ Wed, 22 Apr 2020 09:09:34: 2000000 INFO @ Wed, 22 Apr 2020 09:09:41: 6000000 INFO @ Wed, 22 Apr 2020 09:09:43: 3000000 INFO @ Wed, 22 Apr 2020 09:09:47: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:09:47: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:09:47: #1 total tags in treatment: 1468533 INFO @ Wed, 22 Apr 2020 09:09:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:47: #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 09:09:47: #1 tags after filtering in treatment: 1179868 INFO @ Wed, 22 Apr 2020 09:09:47: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:09:47: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:47: #2 number of paired peaks: 32 WARNING @ Wed, 22 Apr 2020 09:09:47: Too few paired peaks (32) 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 09:09:47: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.10_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/SRX6614962/SRX6614962.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:09:52: 4000000 INFO @ Wed, 22 Apr 2020 09:10:01: 5000000 INFO @ Wed, 22 Apr 2020 09:10:10: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:10:16: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:10:16: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:10:16: #1 total tags in treatment: 1468533 INFO @ Wed, 22 Apr 2020 09:10:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:10:16: #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 09:10:16: #1 tags after filtering in treatment: 1179868 INFO @ Wed, 22 Apr 2020 09:10:16: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:10:16: #1 finished! INFO @ Wed, 22 Apr 2020 09:10:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:10:16: #2 number of paired peaks: 32 WARNING @ Wed, 22 Apr 2020 09:10:16: Too few paired peaks (32) 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 09:10:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.20_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/SRX6614962/SRX6614962.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614962/SRX6614962.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。