Job ID = 5791629 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:12:05 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 ) 2020-04-22T01:14:13 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 : 68,839,641 reads read : 137,679,282 reads written : 137,679,282 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: 00:09:02 68839641 reads; of these: 68839641 (100.00%) were paired; of these: 57478512 (83.50%) aligned concordantly 0 times 10166499 (14.77%) aligned concordantly exactly 1 time 1194630 (1.74%) aligned concordantly >1 times ---- 57478512 pairs aligned concordantly 0 times; of these: 16919 (0.03%) aligned discordantly 1 time ---- 57461593 pairs aligned 0 times concordantly or discordantly; of these: 114923186 mates make up the pairs; of these: 114643256 (99.76%) aligned 0 times 243071 (0.21%) aligned exactly 1 time 36859 (0.03%) aligned >1 times 16.73% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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 12 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] 6047272 / 11368804 = 0.5319 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 10:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.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 10:36:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:36:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:37:01: 1000000 INFO @ Wed, 22 Apr 2020 10:37:08: 2000000 INFO @ Wed, 22 Apr 2020 10:37:14: 3000000 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 10:37:21: 4000000 INFO @ Wed, 22 Apr 2020 10:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.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 10:37:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:37:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:37:28: 5000000 INFO @ Wed, 22 Apr 2020 10:37:32: 1000000 INFO @ Wed, 22 Apr 2020 10:37:36: 6000000 INFO @ Wed, 22 Apr 2020 10:37:38: 2000000 INFO @ Wed, 22 Apr 2020 10:37:43: 7000000 INFO @ Wed, 22 Apr 2020 10:37:45: 3000000 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 10:37:51: 8000000 INFO @ Wed, 22 Apr 2020 10:37:52: 4000000 INFO @ Wed, 22 Apr 2020 10:37:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.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 10:37:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:37:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:37:58: 5000000 INFO @ Wed, 22 Apr 2020 10:37:58: 9000000 INFO @ Wed, 22 Apr 2020 10:38:00: 1000000 INFO @ Wed, 22 Apr 2020 10:38:05: 6000000 INFO @ Wed, 22 Apr 2020 10:38:06: 10000000 INFO @ Wed, 22 Apr 2020 10:38:07: 2000000 INFO @ Wed, 22 Apr 2020 10:38:12: 7000000 INFO @ Wed, 22 Apr 2020 10:38:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:38:13: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:38:13: #1 total tags in treatment: 5318831 INFO @ Wed, 22 Apr 2020 10:38:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:38:13: #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 10:38:13: 3000000 INFO @ Wed, 22 Apr 2020 10:38:13: #1 tags after filtering in treatment: 4290293 INFO @ Wed, 22 Apr 2020 10:38:13: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:38:13: #1 finished! INFO @ Wed, 22 Apr 2020 10:38:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:38:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:38:13: #2 number of paired peaks: 36 WARNING @ Wed, 22 Apr 2020 10:38:13: Too few paired peaks (36) 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 10:38:13: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:38:18: 8000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.05_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/SRX7409597/SRX7409597.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:38:19: 4000000 INFO @ Wed, 22 Apr 2020 10:38:24: 9000000 INFO @ Wed, 22 Apr 2020 10:38:25: 5000000 INFO @ Wed, 22 Apr 2020 10:38:30: 10000000 INFO @ Wed, 22 Apr 2020 10:38:31: 6000000 INFO @ Wed, 22 Apr 2020 10:38:35: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:38:35: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:38:35: #1 total tags in treatment: 5318831 INFO @ Wed, 22 Apr 2020 10:38:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:38:35: #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 10:38:35: #1 tags after filtering in treatment: 4290293 INFO @ Wed, 22 Apr 2020 10:38:35: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:38:35: #1 finished! INFO @ Wed, 22 Apr 2020 10:38:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:38:35: #2 number of paired peaks: 36 WARNING @ Wed, 22 Apr 2020 10:38:35: Too few paired peaks (36) 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 10:38:35: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:38:37: 7000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.10_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/SRX7409597/SRX7409597.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:38:42: 8000000 INFO @ Wed, 22 Apr 2020 10:38:48: 9000000 INFO @ Wed, 22 Apr 2020 10:38:53: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:38:59: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:38:59: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:38:59: #1 total tags in treatment: 5318831 INFO @ Wed, 22 Apr 2020 10:38:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:38:59: #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 10:38:59: #1 tags after filtering in treatment: 4290293 INFO @ Wed, 22 Apr 2020 10:38:59: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:38:59: #1 finished! INFO @ Wed, 22 Apr 2020 10:38:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:38:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:38:59: #2 number of paired peaks: 36 WARNING @ Wed, 22 Apr 2020 10:38:59: Too few paired peaks (36) 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 10:38:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.20_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/SRX7409597/SRX7409597.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409597/SRX7409597.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。