Job ID = 5791157 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:38:30 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 ) 2020-04-21T23:43:28 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 ) 2020-04-21T23:43:28 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 ) 2020-04-21T23:43:28 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 ) 2020-04-21T23:44:00 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 : 12,370,673 reads read : 24,741,346 reads written : 24,741,346 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: 00:15:35 12370673 reads; of these: 12370673 (100.00%) were paired; of these: 7442775 (60.16%) aligned concordantly 0 times 4158825 (33.62%) aligned concordantly exactly 1 time 769073 (6.22%) aligned concordantly >1 times ---- 7442775 pairs aligned concordantly 0 times; of these: 3517543 (47.26%) aligned discordantly 1 time ---- 3925232 pairs aligned 0 times concordantly or discordantly; of these: 7850464 mates make up the pairs; of these: 6492234 (82.70%) aligned 0 times 313210 (3.99%) aligned exactly 1 time 1045020 (13.31%) aligned >1 times 73.76% overall alignment rate Time searching: 00:15:35 Overall time: 00:15:35 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 16 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] 1128796 / 8281373 = 0.1363 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 09:27:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.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 09:27:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:27:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:27:50: 1000000 INFO @ Wed, 22 Apr 2020 09:27:58: 2000000 INFO @ Wed, 22 Apr 2020 09:28:07: 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 09:28:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.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 09:28:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:28:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:28:16: 4000000 INFO @ Wed, 22 Apr 2020 09:28:20: 1000000 INFO @ Wed, 22 Apr 2020 09:28:25: 5000000 INFO @ Wed, 22 Apr 2020 09:28:29: 2000000 INFO @ Wed, 22 Apr 2020 09:28:33: 6000000 INFO @ Wed, 22 Apr 2020 09:28:37: 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 09:28:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.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 09:28:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:28:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:28:42: 7000000 INFO @ Wed, 22 Apr 2020 09:28:44: 4000000 INFO @ Wed, 22 Apr 2020 09:28:49: 1000000 INFO @ Wed, 22 Apr 2020 09:28:51: 8000000 INFO @ Wed, 22 Apr 2020 09:28:51: 5000000 INFO @ Wed, 22 Apr 2020 09:28:56: 2000000 INFO @ Wed, 22 Apr 2020 09:28:58: 6000000 INFO @ Wed, 22 Apr 2020 09:28:59: 9000000 INFO @ Wed, 22 Apr 2020 09:29:04: 3000000 INFO @ Wed, 22 Apr 2020 09:29:06: 7000000 INFO @ Wed, 22 Apr 2020 09:29:08: 10000000 INFO @ Wed, 22 Apr 2020 09:29:11: 4000000 INFO @ Wed, 22 Apr 2020 09:29:13: 8000000 INFO @ Wed, 22 Apr 2020 09:29:17: 11000000 INFO @ Wed, 22 Apr 2020 09:29:18: 5000000 INFO @ Wed, 22 Apr 2020 09:29:20: 9000000 INFO @ Wed, 22 Apr 2020 09:29:25: 12000000 INFO @ Wed, 22 Apr 2020 09:29:25: 6000000 INFO @ Wed, 22 Apr 2020 09:29:27: 10000000 INFO @ Wed, 22 Apr 2020 09:29:32: 7000000 INFO @ Wed, 22 Apr 2020 09:29:34: 13000000 INFO @ Wed, 22 Apr 2020 09:29:35: 11000000 INFO @ Wed, 22 Apr 2020 09:29:40: 8000000 INFO @ Wed, 22 Apr 2020 09:29:42: 12000000 INFO @ Wed, 22 Apr 2020 09:29:42: 14000000 INFO @ Wed, 22 Apr 2020 09:29:47: 9000000 INFO @ Wed, 22 Apr 2020 09:29:49: 13000000 INFO @ Wed, 22 Apr 2020 09:29:51: 15000000 INFO @ Wed, 22 Apr 2020 09:29:54: 10000000 INFO @ Wed, 22 Apr 2020 09:29:56: 14000000 INFO @ Wed, 22 Apr 2020 09:29:59: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:29:59: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:29:59: #1 total tags in treatment: 4302312 INFO @ Wed, 22 Apr 2020 09:29:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:29:59: #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 09:29:59: #1 tags after filtering in treatment: 2871507 INFO @ Wed, 22 Apr 2020 09:29:59: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:29:59: #1 finished! INFO @ Wed, 22 Apr 2020 09:29:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:29:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:30:00: #2 number of paired peaks: 1 WARNING @ Wed, 22 Apr 2020 09:30:00: Too few paired peaks (1) 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 09:30:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.05_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/SRX6614951/SRX6614951.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:30:01: 11000000 INFO @ Wed, 22 Apr 2020 09:30:05: 15000000 INFO @ Wed, 22 Apr 2020 09:30:08: 12000000 INFO @ Wed, 22 Apr 2020 09:30:12: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:30:12: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:30:12: #1 total tags in treatment: 4302312 INFO @ Wed, 22 Apr 2020 09:30:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:30:12: #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 09:30:12: #1 tags after filtering in treatment: 2871507 INFO @ Wed, 22 Apr 2020 09:30:12: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:30:12: #1 finished! INFO @ Wed, 22 Apr 2020 09:30:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:30:12: #2 number of paired peaks: 1 WARNING @ Wed, 22 Apr 2020 09:30:12: Too few paired peaks (1) 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 09:30:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.10_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/SRX6614951/SRX6614951.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:30:15: 13000000 INFO @ Wed, 22 Apr 2020 09:30:22: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:30:29: 15000000 INFO @ Wed, 22 Apr 2020 09:30:36: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:30:36: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:30:36: #1 total tags in treatment: 4302312 INFO @ Wed, 22 Apr 2020 09:30:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:30:36: #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 09:30:36: #1 tags after filtering in treatment: 2871507 INFO @ Wed, 22 Apr 2020 09:30:36: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:30:36: #1 finished! INFO @ Wed, 22 Apr 2020 09:30:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:30:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:30:36: #2 number of paired peaks: 1 WARNING @ Wed, 22 Apr 2020 09:30:36: Too few paired peaks (1) 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 09:30:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.20_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/SRX6614951/SRX6614951.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614951/SRX6614951.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。