Job ID = 5791142 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 ) 2020-04-21T23:38:30 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 ) 2020-04-21T23:38:30 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 ) 2020-04-21T23:38:30 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 ) 2020-04-21T23:38:30 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 ) 2020-04-21T23:47:17 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 ) 2020-04-21T23:48:05 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 ) 2020-04-21T23:48:05 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 : 10,080,641 reads read : 20,161,282 reads written : 20,161,282 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: 00:09:06 10080641 reads; of these: 10080641 (100.00%) were paired; of these: 2639268 (26.18%) aligned concordantly 0 times 3737949 (37.08%) aligned concordantly exactly 1 time 3703424 (36.74%) aligned concordantly >1 times ---- 2639268 pairs aligned concordantly 0 times; of these: 476268 (18.05%) aligned discordantly 1 time ---- 2163000 pairs aligned 0 times concordantly or discordantly; of these: 4326000 mates make up the pairs; of these: 3184080 (73.60%) aligned 0 times 110722 (2.56%) aligned exactly 1 time 1031198 (23.84%) aligned >1 times 84.21% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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] 3631218 / 7851699 = 0.4625 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 09:03:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.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 09:03:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:03:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:03:29: 1000000 INFO @ Wed, 22 Apr 2020 09:03:35: 2000000 INFO @ Wed, 22 Apr 2020 09:03:41: 3000000 INFO @ Wed, 22 Apr 2020 09:03:46: 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 @ Wed, 22 Apr 2020 09:03:52: 5000000 INFO @ Wed, 22 Apr 2020 09:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.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 09:03:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:03:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:03:58: 6000000 INFO @ Wed, 22 Apr 2020 09:03:59: 1000000 INFO @ Wed, 22 Apr 2020 09:04:04: 7000000 INFO @ Wed, 22 Apr 2020 09:04:05: 2000000 INFO @ Wed, 22 Apr 2020 09:04:10: 8000000 INFO @ Wed, 22 Apr 2020 09:04:11: 3000000 INFO @ Wed, 22 Apr 2020 09:04:16: 9000000 INFO @ Wed, 22 Apr 2020 09:04:17: 4000000 INFO @ Wed, 22 Apr 2020 09:04:20: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:04:20: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:04:20: #1 total tags in treatment: 3891854 INFO @ Wed, 22 Apr 2020 09:04:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:04:20: #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 09:04:20: #1 tags after filtering in treatment: 2430081 INFO @ Wed, 22 Apr 2020 09:04:20: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:04:20: #1 finished! INFO @ Wed, 22 Apr 2020 09:04:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:04:20: #2 number of paired peaks: 31 WARNING @ Wed, 22 Apr 2020 09:04:20: Too few paired peaks (31) 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 09:04:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 09:04:23: 5000000 INFO @ Wed, 22 Apr 2020 09:04:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.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 09:04:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:04:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:04:29: 6000000 INFO @ Wed, 22 Apr 2020 09:04:31: 1000000 INFO @ Wed, 22 Apr 2020 09:04:35: 7000000 INFO @ Wed, 22 Apr 2020 09:04:38: 2000000 INFO @ Wed, 22 Apr 2020 09:04:41: 8000000 INFO @ Wed, 22 Apr 2020 09:04:45: 3000000 INFO @ Wed, 22 Apr 2020 09:04:47: 9000000 INFO @ Wed, 22 Apr 2020 09:04:51: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:04:51: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:04:51: #1 total tags in treatment: 3891854 INFO @ Wed, 22 Apr 2020 09:04:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:04:51: #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 09:04:51: #1 tags after filtering in treatment: 2430081 INFO @ Wed, 22 Apr 2020 09:04:51: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:04:51: #1 finished! INFO @ Wed, 22 Apr 2020 09:04:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:04:51: #2 number of paired peaks: 31 WARNING @ Wed, 22 Apr 2020 09:04:51: Too few paired peaks (31) 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 09:04:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.10_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/SRX6614935/SRX6614935.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:04:52: 4000000 INFO @ Wed, 22 Apr 2020 09:04:59: 5000000 INFO @ Wed, 22 Apr 2020 09:05:06: 6000000 INFO @ Wed, 22 Apr 2020 09:05:12: 7000000 INFO @ Wed, 22 Apr 2020 09:05:19: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:05:25: 9000000 INFO @ Wed, 22 Apr 2020 09:05:30: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:05:30: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:05:30: #1 total tags in treatment: 3891854 INFO @ Wed, 22 Apr 2020 09:05:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:05:30: #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 09:05:30: #1 tags after filtering in treatment: 2430081 INFO @ Wed, 22 Apr 2020 09:05:30: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:05:30: #1 finished! INFO @ Wed, 22 Apr 2020 09:05:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:05:30: #2 number of paired peaks: 31 WARNING @ Wed, 22 Apr 2020 09:05:30: Too few paired peaks (31) 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 09:05:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.20_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/SRX6614935/SRX6614935.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614935/SRX6614935.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。