Job ID = 5791170 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:47:14 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 ) 2020-04-21T23:47:14 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 ) 2020-04-22T00:01:26 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 ) 2020-04-22T00:01:26 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 ) 2020-04-22T00:01:26 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 ) 2020-04-22T00:03:38 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 : 12,202,641 reads read : 24,405,282 reads written : 24,405,282 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: 00:15:09 12202641 reads; of these: 12202641 (100.00%) were paired; of these: 7785798 (63.80%) aligned concordantly 0 times 3682023 (30.17%) aligned concordantly exactly 1 time 734820 (6.02%) aligned concordantly >1 times ---- 7785798 pairs aligned concordantly 0 times; of these: 3480341 (44.70%) aligned discordantly 1 time ---- 4305457 pairs aligned 0 times concordantly or discordantly; of these: 8610914 mates make up the pairs; of these: 7199980 (83.61%) aligned 0 times 335703 (3.90%) aligned exactly 1 time 1075231 (12.49%) aligned >1 times 70.50% overall alignment rate Time searching: 00:15:09 Overall time: 00:15:09 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] 1048490 / 7753907 = 0.1352 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 09:28:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.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 09:28:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:28:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:29:05: 1000000 INFO @ Wed, 22 Apr 2020 09:29:13: 2000000 INFO @ Wed, 22 Apr 2020 09:29:20: 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 09:29:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.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 09:29:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:29:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:29:27: 4000000 INFO @ Wed, 22 Apr 2020 09:29:35: 1000000 INFO @ Wed, 22 Apr 2020 09:29:35: 5000000 INFO @ Wed, 22 Apr 2020 09:29:42: 2000000 INFO @ Wed, 22 Apr 2020 09:29:43: 6000000 INFO @ Wed, 22 Apr 2020 09:29:50: 3000000 INFO @ Wed, 22 Apr 2020 09:29:50: 7000000 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 09:29:57: 4000000 INFO @ Wed, 22 Apr 2020 09:29:58: 8000000 INFO @ Wed, 22 Apr 2020 09:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.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 09:29:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:29:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:30:05: 5000000 INFO @ Wed, 22 Apr 2020 09:30:06: 9000000 INFO @ Wed, 22 Apr 2020 09:30:06: 1000000 INFO @ Wed, 22 Apr 2020 09:30:13: 6000000 INFO @ Wed, 22 Apr 2020 09:30:14: 10000000 INFO @ Wed, 22 Apr 2020 09:30:14: 2000000 INFO @ Wed, 22 Apr 2020 09:30:21: 7000000 INFO @ Wed, 22 Apr 2020 09:30:22: 11000000 INFO @ Wed, 22 Apr 2020 09:30:22: 3000000 INFO @ Wed, 22 Apr 2020 09:30:29: 8000000 INFO @ Wed, 22 Apr 2020 09:30:30: 12000000 INFO @ Wed, 22 Apr 2020 09:30:30: 4000000 INFO @ Wed, 22 Apr 2020 09:30:37: 9000000 INFO @ Wed, 22 Apr 2020 09:30:38: 13000000 INFO @ Wed, 22 Apr 2020 09:30:38: 5000000 INFO @ Wed, 22 Apr 2020 09:30:45: 10000000 INFO @ Wed, 22 Apr 2020 09:30:46: 6000000 INFO @ Wed, 22 Apr 2020 09:30:46: 14000000 INFO @ Wed, 22 Apr 2020 09:30:53: 11000000 INFO @ Wed, 22 Apr 2020 09:30:54: 7000000 INFO @ Wed, 22 Apr 2020 09:30:54: 15000000 INFO @ Wed, 22 Apr 2020 09:30:55: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:30:55: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:30:55: #1 total tags in treatment: 3859120 INFO @ Wed, 22 Apr 2020 09:30:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:30:55: #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 09:30:55: #1 tags after filtering in treatment: 2614150 INFO @ Wed, 22 Apr 2020 09:30:55: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Apr 2020 09:30:55: #1 finished! INFO @ Wed, 22 Apr 2020 09:30:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:30:55: #2 number of paired peaks: 3 WARNING @ Wed, 22 Apr 2020 09:30:55: Too few paired peaks (3) 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 09:30:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.05_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/SRX6614963/SRX6614963.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:31:01: 12000000 INFO @ Wed, 22 Apr 2020 09:31:02: 8000000 INFO @ Wed, 22 Apr 2020 09:31:09: 13000000 INFO @ Wed, 22 Apr 2020 09:31:10: 9000000 INFO @ Wed, 22 Apr 2020 09:31:17: 14000000 INFO @ Wed, 22 Apr 2020 09:31:17: 10000000 INFO @ Wed, 22 Apr 2020 09:31:25: 15000000 INFO @ Wed, 22 Apr 2020 09:31:25: 11000000 INFO @ Wed, 22 Apr 2020 09:31:26: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:31:26: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:31:26: #1 total tags in treatment: 3859120 INFO @ Wed, 22 Apr 2020 09:31:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:31:26: #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 09:31:26: #1 tags after filtering in treatment: 2614150 INFO @ Wed, 22 Apr 2020 09:31:26: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Apr 2020 09:31:26: #1 finished! INFO @ Wed, 22 Apr 2020 09:31:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:31:26: #2 number of paired peaks: 3 WARNING @ Wed, 22 Apr 2020 09:31:26: Too few paired peaks (3) 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 09:31:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.10_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/SRX6614963/SRX6614963.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:31:33: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:31:41: 13000000 INFO @ Wed, 22 Apr 2020 09:31:49: 14000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:31:57: 15000000 INFO @ Wed, 22 Apr 2020 09:31:58: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:31:58: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:31:58: #1 total tags in treatment: 3859120 INFO @ Wed, 22 Apr 2020 09:31:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:31:58: #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 09:31:58: #1 tags after filtering in treatment: 2614150 INFO @ Wed, 22 Apr 2020 09:31:58: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Apr 2020 09:31:58: #1 finished! INFO @ Wed, 22 Apr 2020 09:31:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:31:58: #2 number of paired peaks: 3 WARNING @ Wed, 22 Apr 2020 09:31:58: Too few paired peaks (3) 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 09:31:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.20_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/SRX6614963/SRX6614963.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614963/SRX6614963.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling