Job ID = 5791280 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:25:34 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 ) 2020-04-22T00:25:34 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 : 23,151,849 reads read : 46,303,698 reads written : 46,303,698 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: 00:08:58 23151849 reads; of these: 23151849 (100.00%) were paired; of these: 6886291 (29.74%) aligned concordantly 0 times 14663195 (63.33%) aligned concordantly exactly 1 time 1602363 (6.92%) aligned concordantly >1 times ---- 6886291 pairs aligned concordantly 0 times; of these: 45407 (0.66%) aligned discordantly 1 time ---- 6840884 pairs aligned 0 times concordantly or discordantly; of these: 13681768 mates make up the pairs; of these: 13310403 (97.29%) aligned 0 times 319993 (2.34%) aligned exactly 1 time 51372 (0.38%) aligned >1 times 71.25% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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] 8182776 / 16273651 = 0.5028 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 09:53:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.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 09:53:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:53:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:54:01: 1000000 INFO @ Wed, 22 Apr 2020 09:54:07: 2000000 INFO @ Wed, 22 Apr 2020 09:54:13: 3000000 INFO @ Wed, 22 Apr 2020 09:54:19: 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 09:54:25: 5000000 INFO @ Wed, 22 Apr 2020 09:54:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.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 09:54:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:54:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:54:31: 6000000 INFO @ Wed, 22 Apr 2020 09:54:31: 1000000 INFO @ Wed, 22 Apr 2020 09:54:36: 2000000 INFO @ Wed, 22 Apr 2020 09:54:37: 7000000 INFO @ Wed, 22 Apr 2020 09:54:42: 3000000 INFO @ Wed, 22 Apr 2020 09:54:43: 8000000 INFO @ Wed, 22 Apr 2020 09:54:47: 4000000 INFO @ Wed, 22 Apr 2020 09:54:49: 9000000 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 09:54:53: 5000000 INFO @ Wed, 22 Apr 2020 09:54:55: 10000000 INFO @ Wed, 22 Apr 2020 09:54:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.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 09:54:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:54:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:54:58: 6000000 INFO @ Wed, 22 Apr 2020 09:55:01: 11000000 INFO @ Wed, 22 Apr 2020 09:55:01: 1000000 INFO @ Wed, 22 Apr 2020 09:55:03: 7000000 INFO @ Wed, 22 Apr 2020 09:55:06: 2000000 INFO @ Wed, 22 Apr 2020 09:55:07: 12000000 INFO @ Wed, 22 Apr 2020 09:55:09: 8000000 INFO @ Wed, 22 Apr 2020 09:55:12: 3000000 INFO @ Wed, 22 Apr 2020 09:55:13: 13000000 INFO @ Wed, 22 Apr 2020 09:55:14: 9000000 INFO @ Wed, 22 Apr 2020 09:55:17: 4000000 INFO @ Wed, 22 Apr 2020 09:55:19: 14000000 INFO @ Wed, 22 Apr 2020 09:55:20: 10000000 INFO @ Wed, 22 Apr 2020 09:55:23: 5000000 INFO @ Wed, 22 Apr 2020 09:55:25: 15000000 INFO @ Wed, 22 Apr 2020 09:55:25: 11000000 INFO @ Wed, 22 Apr 2020 09:55:28: 6000000 INFO @ Wed, 22 Apr 2020 09:55:30: 12000000 INFO @ Wed, 22 Apr 2020 09:55:31: 16000000 INFO @ Wed, 22 Apr 2020 09:55:34: 7000000 INFO @ Wed, 22 Apr 2020 09:55:34: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:55:34: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:55:34: #1 total tags in treatment: 8085745 INFO @ Wed, 22 Apr 2020 09:55:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:55:34: #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 09:55:34: #1 tags after filtering in treatment: 6473064 INFO @ Wed, 22 Apr 2020 09:55:34: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:55:34: #1 finished! INFO @ Wed, 22 Apr 2020 09:55:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:55:35: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:55:35: Too few paired peaks (0) 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 09:55:35: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:55:36: 13000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.05_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/SRX7409539/SRX7409539.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:55:39: 8000000 INFO @ Wed, 22 Apr 2020 09:55:41: 14000000 INFO @ Wed, 22 Apr 2020 09:55:44: 9000000 INFO @ Wed, 22 Apr 2020 09:55:46: 15000000 INFO @ Wed, 22 Apr 2020 09:55:50: 10000000 INFO @ Wed, 22 Apr 2020 09:55:51: 16000000 INFO @ Wed, 22 Apr 2020 09:55:55: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:55:55: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:55:55: #1 total tags in treatment: 8085745 INFO @ Wed, 22 Apr 2020 09:55:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:55:55: #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 09:55:55: #1 tags after filtering in treatment: 6473064 INFO @ Wed, 22 Apr 2020 09:55:55: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:55:55: #1 finished! INFO @ Wed, 22 Apr 2020 09:55:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:55:55: 11000000 INFO @ Wed, 22 Apr 2020 09:55:55: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:55:55: Too few paired peaks (0) 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 09:55:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.10_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/SRX7409539/SRX7409539.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:56:00: 12000000 INFO @ Wed, 22 Apr 2020 09:56:05: 13000000 INFO @ Wed, 22 Apr 2020 09:56:10: 14000000 INFO @ Wed, 22 Apr 2020 09:56:15: 15000000 INFO @ Wed, 22 Apr 2020 09:56:20: 16000000 INFO @ Wed, 22 Apr 2020 09:56:23: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:56:23: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:56:23: #1 total tags in treatment: 8085745 INFO @ Wed, 22 Apr 2020 09:56:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:56:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:56:23: #1 tags after filtering in treatment: 6473064 INFO @ Wed, 22 Apr 2020 09:56:23: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:56:23: #1 finished! INFO @ Wed, 22 Apr 2020 09:56:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:56:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:56:23: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:56:23: Too few paired peaks (0) 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 09:56:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.20_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/SRX7409539/SRX7409539.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409539/SRX7409539.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。