Job ID = 5791269 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:17:06 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 ) 2020-04-22T00:20:41 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 : 10,420,571 reads read : 20,841,142 reads written : 20,841,142 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: 00:03:53 10420571 reads; of these: 10420571 (100.00%) were paired; of these: 3815327 (36.61%) aligned concordantly 0 times 4718085 (45.28%) aligned concordantly exactly 1 time 1887159 (18.11%) aligned concordantly >1 times ---- 3815327 pairs aligned concordantly 0 times; of these: 394230 (10.33%) aligned discordantly 1 time ---- 3421097 pairs aligned 0 times concordantly or discordantly; of these: 6842194 mates make up the pairs; of these: 5811765 (84.94%) aligned 0 times 640477 (9.36%) aligned exactly 1 time 389952 (5.70%) aligned >1 times 72.11% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 1227905 / 6889590 = 0.1782 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 09:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.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 09:36:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:36:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:36:56: 1000000 INFO @ Wed, 22 Apr 2020 09:37:00: 2000000 INFO @ Wed, 22 Apr 2020 09:37:05: 3000000 INFO @ Wed, 22 Apr 2020 09:37:10: 4000000 INFO @ Wed, 22 Apr 2020 09:37:14: 5000000 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 09:37:19: 6000000 INFO @ Wed, 22 Apr 2020 09:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.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 09:37:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:24: 7000000 INFO @ Wed, 22 Apr 2020 09:37:28: 1000000 INFO @ Wed, 22 Apr 2020 09:37:30: 8000000 INFO @ Wed, 22 Apr 2020 09:37:35: 2000000 INFO @ Wed, 22 Apr 2020 09:37:36: 9000000 INFO @ Wed, 22 Apr 2020 09:37:41: 3000000 INFO @ Wed, 22 Apr 2020 09:37:41: 10000000 INFO @ Wed, 22 Apr 2020 09:37:47: 11000000 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 09:37:48: 4000000 INFO @ Wed, 22 Apr 2020 09:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.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 09:37:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:53: 12000000 INFO @ Wed, 22 Apr 2020 09:37:54: 5000000 INFO @ Wed, 22 Apr 2020 09:37:56: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:37:56: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:37:56: #1 total tags in treatment: 5431017 INFO @ Wed, 22 Apr 2020 09:37:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:37:56: #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 09:37:56: #1 tags after filtering in treatment: 3765580 INFO @ Wed, 22 Apr 2020 09:37:56: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Apr 2020 09:37:56: #1 finished! INFO @ Wed, 22 Apr 2020 09:37:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:37:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:37:57: 1000000 INFO @ Wed, 22 Apr 2020 09:37:57: #2 number of paired peaks: 31 WARNING @ Wed, 22 Apr 2020 09:37:57: 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 09:37:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.05_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/SRX7399901/SRX7399901.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:38:01: 6000000 INFO @ Wed, 22 Apr 2020 09:38:02: 2000000 INFO @ Wed, 22 Apr 2020 09:38:08: 7000000 INFO @ Wed, 22 Apr 2020 09:38:08: 3000000 INFO @ Wed, 22 Apr 2020 09:38:14: 4000000 INFO @ Wed, 22 Apr 2020 09:38:14: 8000000 INFO @ Wed, 22 Apr 2020 09:38:20: 5000000 INFO @ Wed, 22 Apr 2020 09:38:21: 9000000 INFO @ Wed, 22 Apr 2020 09:38:26: 6000000 INFO @ Wed, 22 Apr 2020 09:38:28: 10000000 INFO @ Wed, 22 Apr 2020 09:38:32: 7000000 INFO @ Wed, 22 Apr 2020 09:38:34: 11000000 INFO @ Wed, 22 Apr 2020 09:38:38: 8000000 INFO @ Wed, 22 Apr 2020 09:38:41: 12000000 INFO @ Wed, 22 Apr 2020 09:38:43: 9000000 INFO @ Wed, 22 Apr 2020 09:38:45: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:38:45: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:38:45: #1 total tags in treatment: 5431017 INFO @ Wed, 22 Apr 2020 09:38:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:38:45: #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 09:38:45: #1 tags after filtering in treatment: 3765580 INFO @ Wed, 22 Apr 2020 09:38:45: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Apr 2020 09:38:45: #1 finished! INFO @ Wed, 22 Apr 2020 09:38:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:38:45: #2 number of paired peaks: 31 WARNING @ Wed, 22 Apr 2020 09:38:45: 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 09:38:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.10_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/SRX7399901/SRX7399901.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:38:49: 10000000 INFO @ Wed, 22 Apr 2020 09:38:54: 11000000 INFO @ Wed, 22 Apr 2020 09:38:59: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:39:02: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:39:02: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:39:02: #1 total tags in treatment: 5431017 INFO @ Wed, 22 Apr 2020 09:39:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:39:02: #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 09:39:02: #1 tags after filtering in treatment: 3765580 INFO @ Wed, 22 Apr 2020 09:39:02: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 22 Apr 2020 09:39:02: #1 finished! INFO @ Wed, 22 Apr 2020 09:39:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:39:02: #2 number of paired peaks: 31 WARNING @ Wed, 22 Apr 2020 09:39:02: 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 09:39:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.20_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/SRX7399901/SRX7399901.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399901/SRX7399901.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。