Job ID = 5791271 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:27:42 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 ) 2020-04-22T00:27:42 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 ) 2020-04-22T00:29:48 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 ) 2020-04-22T00:29:48 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 : 22,466,252 reads read : 44,932,504 reads written : 44,932,504 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: 00:03:17 22466252 reads; of these: 22466252 (100.00%) were paired; of these: 21773811 (96.92%) aligned concordantly 0 times 534741 (2.38%) aligned concordantly exactly 1 time 157700 (0.70%) aligned concordantly >1 times ---- 21773811 pairs aligned concordantly 0 times; of these: 577156 (2.65%) aligned discordantly 1 time ---- 21196655 pairs aligned 0 times concordantly or discordantly; of these: 42393310 mates make up the pairs; of these: 40529632 (95.60%) aligned 0 times 1337078 (3.15%) aligned exactly 1 time 526600 (1.24%) aligned >1 times 9.80% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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_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] 986848 / 1232757 = 0.8005 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 09:37:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.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 09:37:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:32: 1000000 INFO @ Wed, 22 Apr 2020 09:37:37: 2000000 INFO @ Wed, 22 Apr 2020 09:37:40: #1 tag size is determined as 43 bps INFO @ Wed, 22 Apr 2020 09:37:40: #1 tag size = 43 INFO @ Wed, 22 Apr 2020 09:37:40: #1 total tags in treatment: 142853 INFO @ Wed, 22 Apr 2020 09:37:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:37:40: #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 09:37:40: #1 tags after filtering in treatment: 128495 INFO @ Wed, 22 Apr 2020 09:37:40: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 22 Apr 2020 09:37:40: #1 finished! INFO @ Wed, 22 Apr 2020 09:37:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:37:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:37:40: #2 number of paired peaks: 56 WARNING @ Wed, 22 Apr 2020 09:37:40: Too few paired peaks (56) 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 09:37:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.05_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/SRX7399903/SRX7399903.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 09:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.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 09:37:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:38:02: 1000000 INFO @ Wed, 22 Apr 2020 09:38:08: 2000000 INFO @ Wed, 22 Apr 2020 09:38:10: #1 tag size is determined as 43 bps INFO @ Wed, 22 Apr 2020 09:38:10: #1 tag size = 43 INFO @ Wed, 22 Apr 2020 09:38:10: #1 total tags in treatment: 142853 INFO @ Wed, 22 Apr 2020 09:38:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:38:10: #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 09:38:10: #1 tags after filtering in treatment: 128495 INFO @ Wed, 22 Apr 2020 09:38:10: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 22 Apr 2020 09:38:10: #1 finished! INFO @ Wed, 22 Apr 2020 09:38:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:38:10: #2 number of paired peaks: 56 WARNING @ Wed, 22 Apr 2020 09:38:10: Too few paired peaks (56) 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 09:38:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.10_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/SRX7399903/SRX7399903.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.10_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 09:38:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.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 09:38:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:38:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:38:31: 1000000 INFO @ Wed, 22 Apr 2020 09:38:36: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:38:38: #1 tag size is determined as 43 bps INFO @ Wed, 22 Apr 2020 09:38:38: #1 tag size = 43 INFO @ Wed, 22 Apr 2020 09:38:38: #1 total tags in treatment: 142853 INFO @ Wed, 22 Apr 2020 09:38:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:38:38: #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 09:38:38: #1 tags after filtering in treatment: 128495 INFO @ Wed, 22 Apr 2020 09:38:38: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 22 Apr 2020 09:38:38: #1 finished! INFO @ Wed, 22 Apr 2020 09:38:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:38:38: #2 number of paired peaks: 56 WARNING @ Wed, 22 Apr 2020 09:38:38: Too few paired peaks (56) 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 09:38:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.20_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/SRX7399903/SRX7399903.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399903/SRX7399903.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。