Job ID = 5790853 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T22:55:24 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 ) 2020-04-21T22:55:24 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 : 3,961,384 reads read : 7,922,768 reads written : 7,922,768 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: 00:01:43 3961384 reads; of these: 3961384 (100.00%) were paired; of these: 75592 (1.91%) aligned concordantly 0 times 3410981 (86.11%) aligned concordantly exactly 1 time 474811 (11.99%) aligned concordantly >1 times ---- 75592 pairs aligned concordantly 0 times; of these: 2502 (3.31%) aligned discordantly 1 time ---- 73090 pairs aligned 0 times concordantly or discordantly; of these: 146180 mates make up the pairs; of these: 121822 (83.34%) aligned 0 times 20158 (13.79%) aligned exactly 1 time 4200 (2.87%) aligned >1 times 98.46% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 79713 / 3886443 = 0.0205 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 07:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.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 07:59:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:59:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:59:58: 1000000 INFO @ Wed, 22 Apr 2020 08:00:03: 2000000 INFO @ Wed, 22 Apr 2020 08:00:08: 3000000 INFO @ Wed, 22 Apr 2020 08:00:20: 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 08:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.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 08:00:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:31: 1000000 INFO @ Wed, 22 Apr 2020 08:00:32: 5000000 INFO @ Wed, 22 Apr 2020 08:00:36: 2000000 INFO @ Wed, 22 Apr 2020 08:00:37: 6000000 INFO @ Wed, 22 Apr 2020 08:00:41: 3000000 INFO @ Wed, 22 Apr 2020 08:00:43: 7000000 INFO @ Wed, 22 Apr 2020 08:00:46: 4000000 INFO @ Wed, 22 Apr 2020 08:00:46: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:00:46: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:00:46: #1 total tags in treatment: 3806100 INFO @ Wed, 22 Apr 2020 08:00:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:00:46: #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 08:00:46: #1 tags after filtering in treatment: 3070883 INFO @ Wed, 22 Apr 2020 08:00:46: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:00:46: #1 finished! INFO @ Wed, 22 Apr 2020 08:00:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:00:46: #2 number of paired peaks: 99 WARNING @ Wed, 22 Apr 2020 08:00:46: Too few paired peaks (99) 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 08:00:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.05_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/SRX5521501/SRX5521501.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:00:50: 5000000 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 08:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.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 08:00:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:55: 6000000 INFO @ Wed, 22 Apr 2020 08:01:00: 7000000 INFO @ Wed, 22 Apr 2020 08:01:00: 1000000 INFO @ Wed, 22 Apr 2020 08:01:03: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:01:03: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:01:03: #1 total tags in treatment: 3806100 INFO @ Wed, 22 Apr 2020 08:01:03: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:01:03: #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 08:01:03: #1 tags after filtering in treatment: 3070883 INFO @ Wed, 22 Apr 2020 08:01:03: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:01:03: #1 finished! INFO @ Wed, 22 Apr 2020 08:01:03: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:01:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:01:03: #2 number of paired peaks: 99 WARNING @ Wed, 22 Apr 2020 08:01:03: Too few paired peaks (99) 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 08:01:03: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 08:01:05: 2000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:01:11: 3000000 INFO @ Wed, 22 Apr 2020 08:01:17: 4000000 INFO @ Wed, 22 Apr 2020 08:01:27: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:01:41: 6000000 INFO @ Wed, 22 Apr 2020 08:01:47: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:01:50: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:01:50: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:01:50: #1 total tags in treatment: 3806100 INFO @ Wed, 22 Apr 2020 08:01:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:01:50: #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 08:01:50: #1 tags after filtering in treatment: 3070883 INFO @ Wed, 22 Apr 2020 08:01:50: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:01:50: #1 finished! INFO @ Wed, 22 Apr 2020 08:01:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:01:50: #2 number of paired peaks: 99 WARNING @ Wed, 22 Apr 2020 08:01:50: Too few paired peaks (99) 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 08:01:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.20_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/SRX5521501/SRX5521501.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5521501/SRX5521501.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling