Job ID = 5791171 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:46:27 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 ) 2020-04-21T23:46:27 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 : 7,227,401 reads read : 14,454,802 reads written : 14,454,802 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: 00:07:11 7227401 reads; of these: 7227401 (100.00%) were paired; of these: 5261107 (72.79%) aligned concordantly 0 times 1707505 (23.63%) aligned concordantly exactly 1 time 258789 (3.58%) aligned concordantly >1 times ---- 5261107 pairs aligned concordantly 0 times; of these: 1713990 (32.58%) aligned discordantly 1 time ---- 3547117 pairs aligned 0 times concordantly or discordantly; of these: 7094234 mates make up the pairs; of these: 6517279 (91.87%) aligned 0 times 140437 (1.98%) aligned exactly 1 time 436518 (6.15%) aligned >1 times 54.91% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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] 619451 / 3611151 = 0.1715 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 09:07:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.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 09:07:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:07:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:07:09: 1000000 INFO @ Wed, 22 Apr 2020 09:07:18: 2000000 INFO @ Wed, 22 Apr 2020 09:07:28: 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 09:07:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.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 09:07:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:07:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:07:38: 4000000 INFO @ Wed, 22 Apr 2020 09:07:43: 1000000 INFO @ Wed, 22 Apr 2020 09:07:50: 5000000 INFO @ Wed, 22 Apr 2020 09:07:54: 2000000 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 09:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.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 09:08:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:08:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:08:01: 6000000 INFO @ Wed, 22 Apr 2020 09:08:05: 3000000 INFO @ Wed, 22 Apr 2020 09:08:08: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:08:08: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:08:08: #1 total tags in treatment: 1589915 INFO @ Wed, 22 Apr 2020 09:08:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:08:08: #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 09:08:08: #1 tags after filtering in treatment: 1295224 INFO @ Wed, 22 Apr 2020 09:08:08: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 09:08:08: #1 finished! INFO @ Wed, 22 Apr 2020 09:08:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:08:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:08:08: #2 number of paired peaks: 17 WARNING @ Wed, 22 Apr 2020 09:08:08: Too few paired peaks (17) 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 09:08:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.05_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/SRX6614964/SRX6614964.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:08:11: 1000000 INFO @ Wed, 22 Apr 2020 09:08:16: 4000000 INFO @ Wed, 22 Apr 2020 09:08:22: 2000000 INFO @ Wed, 22 Apr 2020 09:08:27: 5000000 INFO @ Wed, 22 Apr 2020 09:08:33: 3000000 INFO @ Wed, 22 Apr 2020 09:08:38: 6000000 INFO @ Wed, 22 Apr 2020 09:08:44: 4000000 INFO @ Wed, 22 Apr 2020 09:08:45: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:08:45: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:08:45: #1 total tags in treatment: 1589915 INFO @ Wed, 22 Apr 2020 09:08:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:08:45: #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 09:08:45: #1 tags after filtering in treatment: 1295224 INFO @ Wed, 22 Apr 2020 09:08:45: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 09:08:45: #1 finished! INFO @ Wed, 22 Apr 2020 09:08:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:08:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:08:45: #2 number of paired peaks: 17 WARNING @ Wed, 22 Apr 2020 09:08:45: Too few paired peaks (17) 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 09:08:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.10_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/SRX6614964/SRX6614964.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:08:54: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:09:04: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:09:10: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:09:10: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:09:10: #1 total tags in treatment: 1589915 INFO @ Wed, 22 Apr 2020 09:09:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:10: #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 09:09:10: #1 tags after filtering in treatment: 1295224 INFO @ Wed, 22 Apr 2020 09:09:10: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 09:09:10: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:10: #2 number of paired peaks: 17 WARNING @ Wed, 22 Apr 2020 09:09:10: Too few paired peaks (17) 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 09:09:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.20_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/SRX6614964/SRX6614964.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614964/SRX6614964.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling