Job ID = 5791197 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:59:27 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 ) 2020-04-21T23:59:27 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 : 12,556,284 reads read : 25,112,568 reads written : 25,112,568 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: 00:11:59 12556284 reads; of these: 12556284 (100.00%) were paired; of these: 2911836 (23.19%) aligned concordantly 0 times 5707214 (45.45%) aligned concordantly exactly 1 time 3937234 (31.36%) aligned concordantly >1 times ---- 2911836 pairs aligned concordantly 0 times; of these: 723548 (24.85%) aligned discordantly 1 time ---- 2188288 pairs aligned 0 times concordantly or discordantly; of these: 4376576 mates make up the pairs; of these: 3317919 (75.81%) aligned 0 times 147448 (3.37%) aligned exactly 1 time 911209 (20.82%) aligned >1 times 86.79% overall alignment rate Time searching: 00:11:59 Overall time: 00:11:59 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] 3835488 / 10274398 = 0.3733 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 09:28:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.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 09:28:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:28:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:28:22: 1000000 INFO @ Wed, 22 Apr 2020 09:28:28: 2000000 INFO @ Wed, 22 Apr 2020 09:28:34: 3000000 INFO @ Wed, 22 Apr 2020 09:28:41: 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 09:28:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.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 09:28:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:28:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:28:47: 5000000 INFO @ Wed, 22 Apr 2020 09:28:52: 1000000 INFO @ Wed, 22 Apr 2020 09:28:54: 6000000 INFO @ Wed, 22 Apr 2020 09:28:59: 2000000 INFO @ Wed, 22 Apr 2020 09:29:01: 7000000 INFO @ Wed, 22 Apr 2020 09:29:06: 3000000 INFO @ Wed, 22 Apr 2020 09:29:08: 8000000 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 09:29:13: 4000000 INFO @ Wed, 22 Apr 2020 09:29:15: 9000000 INFO @ Wed, 22 Apr 2020 09:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.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 09:29:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:29:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:29:20: 5000000 INFO @ Wed, 22 Apr 2020 09:29:22: 10000000 INFO @ Wed, 22 Apr 2020 09:29:22: 1000000 INFO @ Wed, 22 Apr 2020 09:29:27: 6000000 INFO @ Wed, 22 Apr 2020 09:29:29: 11000000 INFO @ Wed, 22 Apr 2020 09:29:29: 2000000 INFO @ Wed, 22 Apr 2020 09:29:34: 7000000 INFO @ Wed, 22 Apr 2020 09:29:36: 12000000 INFO @ Wed, 22 Apr 2020 09:29:36: 3000000 INFO @ Wed, 22 Apr 2020 09:29:41: 8000000 INFO @ Wed, 22 Apr 2020 09:29:43: 13000000 INFO @ Wed, 22 Apr 2020 09:29:44: 4000000 INFO @ Wed, 22 Apr 2020 09:29:48: 9000000 INFO @ Wed, 22 Apr 2020 09:29:50: 14000000 INFO @ Wed, 22 Apr 2020 09:29:51: 5000000 INFO @ Wed, 22 Apr 2020 09:29:51: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:29:51: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:29:51: #1 total tags in treatment: 5919500 INFO @ Wed, 22 Apr 2020 09:29:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:29:51: #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 09:29:51: #1 tags after filtering in treatment: 3448081 INFO @ Wed, 22 Apr 2020 09:29:51: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 09:29:51: #1 finished! INFO @ Wed, 22 Apr 2020 09:29:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:29:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:29:51: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 09:29:51: Too few paired peaks (26) 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 09:29:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:29:55: 10000000 INFO @ Wed, 22 Apr 2020 09:29:58: 6000000 INFO @ Wed, 22 Apr 2020 09:30:02: 11000000 INFO @ Wed, 22 Apr 2020 09:30:05: 7000000 INFO @ Wed, 22 Apr 2020 09:30:09: 12000000 INFO @ Wed, 22 Apr 2020 09:30:12: 8000000 INFO @ Wed, 22 Apr 2020 09:30:16: 13000000 INFO @ Wed, 22 Apr 2020 09:30:19: 9000000 INFO @ Wed, 22 Apr 2020 09:30:23: 14000000 INFO @ Wed, 22 Apr 2020 09:30:24: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:30:24: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:30:24: #1 total tags in treatment: 5919500 INFO @ Wed, 22 Apr 2020 09:30:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:30:24: #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 09:30:24: #1 tags after filtering in treatment: 3448081 INFO @ Wed, 22 Apr 2020 09:30:24: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 09:30:24: #1 finished! INFO @ Wed, 22 Apr 2020 09:30:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:30:24: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 09:30:24: Too few paired peaks (26) 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 09:30:24: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:30:26: 10000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.10_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/SRX6614988/SRX6614988.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:30:32: 11000000 INFO @ Wed, 22 Apr 2020 09:30:38: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:30:45: 13000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:30:52: 14000000 INFO @ Wed, 22 Apr 2020 09:30:52: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:30:52: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:30:52: #1 total tags in treatment: 5919500 INFO @ Wed, 22 Apr 2020 09:30:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:30:52: #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 09:30:53: #1 tags after filtering in treatment: 3448081 INFO @ Wed, 22 Apr 2020 09:30:53: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Apr 2020 09:30:53: #1 finished! INFO @ Wed, 22 Apr 2020 09:30:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:30:53: #2 number of paired peaks: 26 WARNING @ Wed, 22 Apr 2020 09:30:53: Too few paired peaks (26) 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 09:30:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.20_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/SRX6614988/SRX6614988.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614988/SRX6614988.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling