Job ID = 5791667 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:18:12 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 ) 2020-04-22T01:20:01 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 ) 2020-04-22T01:20:03 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 ) 2020-04-22T01:20:14 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 ) 2020-04-22T01:20:14 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 ) 2020-04-22T01:35:34 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 ) 2020-04-22T01:35:34 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 : 30,798,583 reads read : 61,597,166 reads written : 61,597,166 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: 00:14:53 30798583 reads; of these: 30798583 (100.00%) were paired; of these: 13601575 (44.16%) aligned concordantly 0 times 14209714 (46.14%) aligned concordantly exactly 1 time 2987294 (9.70%) aligned concordantly >1 times ---- 13601575 pairs aligned concordantly 0 times; of these: 7755 (0.06%) aligned discordantly 1 time ---- 13593820 pairs aligned 0 times concordantly or discordantly; of these: 27187640 mates make up the pairs; of these: 26888542 (98.90%) aligned 0 times 219591 (0.81%) aligned exactly 1 time 79507 (0.29%) aligned >1 times 56.35% overall alignment rate Time searching: 00:14:53 Overall time: 00:14:53 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 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] 6114739 / 17200878 = 0.3555 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 10:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.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 10:59:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:59:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:59:46: 1000000 INFO @ Wed, 22 Apr 2020 10:59:51: 2000000 INFO @ Wed, 22 Apr 2020 10:59:55: 3000000 INFO @ Wed, 22 Apr 2020 11:00:00: 4000000 INFO @ Wed, 22 Apr 2020 11:00:04: 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 11:00:08: 6000000 INFO @ Wed, 22 Apr 2020 11:00:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.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 11:00:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:00:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:00:13: 7000000 INFO @ Wed, 22 Apr 2020 11:00:16: 1000000 INFO @ Wed, 22 Apr 2020 11:00:17: 8000000 INFO @ Wed, 22 Apr 2020 11:00:21: 2000000 INFO @ Wed, 22 Apr 2020 11:00:22: 9000000 INFO @ Wed, 22 Apr 2020 11:00:26: 3000000 INFO @ Wed, 22 Apr 2020 11:00:27: 10000000 INFO @ Wed, 22 Apr 2020 11:00:30: 4000000 INFO @ Wed, 22 Apr 2020 11:00:32: 11000000 INFO @ Wed, 22 Apr 2020 11:00:35: 5000000 INFO @ Wed, 22 Apr 2020 11:00:36: 12000000 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 11:00:40: 6000000 INFO @ Wed, 22 Apr 2020 11:00:41: 13000000 INFO @ Wed, 22 Apr 2020 11:00:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.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 11:00:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:00:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:00:44: 7000000 INFO @ Wed, 22 Apr 2020 11:00:46: 14000000 INFO @ Wed, 22 Apr 2020 11:00:46: 1000000 INFO @ Wed, 22 Apr 2020 11:00:49: 8000000 INFO @ Wed, 22 Apr 2020 11:00:50: 15000000 INFO @ Wed, 22 Apr 2020 11:00:51: 2000000 INFO @ Wed, 22 Apr 2020 11:00:54: 9000000 INFO @ Wed, 22 Apr 2020 11:00:55: 16000000 INFO @ Wed, 22 Apr 2020 11:00:56: 3000000 INFO @ Wed, 22 Apr 2020 11:00:58: 10000000 INFO @ Wed, 22 Apr 2020 11:01:00: 17000000 INFO @ Wed, 22 Apr 2020 11:01:01: 4000000 INFO @ Wed, 22 Apr 2020 11:01:03: 11000000 INFO @ Wed, 22 Apr 2020 11:01:04: 18000000 INFO @ Wed, 22 Apr 2020 11:01:05: 5000000 INFO @ Wed, 22 Apr 2020 11:01:08: 12000000 INFO @ Wed, 22 Apr 2020 11:01:09: 19000000 INFO @ Wed, 22 Apr 2020 11:01:10: 6000000 INFO @ Wed, 22 Apr 2020 11:01:12: 13000000 INFO @ Wed, 22 Apr 2020 11:01:14: 20000000 INFO @ Wed, 22 Apr 2020 11:01:15: 7000000 INFO @ Wed, 22 Apr 2020 11:01:17: 14000000 INFO @ Wed, 22 Apr 2020 11:01:18: 21000000 INFO @ Wed, 22 Apr 2020 11:01:20: 8000000 INFO @ Wed, 22 Apr 2020 11:01:22: 15000000 INFO @ Wed, 22 Apr 2020 11:01:23: 22000000 INFO @ Wed, 22 Apr 2020 11:01:24: 9000000 INFO @ Wed, 22 Apr 2020 11:01:25: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:01:25: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:01:25: #1 total tags in treatment: 11083477 INFO @ Wed, 22 Apr 2020 11:01:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:01:25: #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 11:01:26: #1 tags after filtering in treatment: 6074474 INFO @ Wed, 22 Apr 2020 11:01:26: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 11:01:26: #1 finished! INFO @ Wed, 22 Apr 2020 11:01:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:01:26: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:01:26: Too few paired peaks (0) 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 11:01:26: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 11:01:27: 16000000 INFO @ Wed, 22 Apr 2020 11:01:29: 10000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.05_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/SRX7409629/SRX7409629.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:01:31: 17000000 INFO @ Wed, 22 Apr 2020 11:01:34: 11000000 INFO @ Wed, 22 Apr 2020 11:01:36: 18000000 INFO @ Wed, 22 Apr 2020 11:01:39: 12000000 INFO @ Wed, 22 Apr 2020 11:01:41: 19000000 INFO @ Wed, 22 Apr 2020 11:01:43: 13000000 INFO @ Wed, 22 Apr 2020 11:01:45: 20000000 INFO @ Wed, 22 Apr 2020 11:01:48: 14000000 INFO @ Wed, 22 Apr 2020 11:01:50: 21000000 INFO @ Wed, 22 Apr 2020 11:01:53: 15000000 INFO @ Wed, 22 Apr 2020 11:01:55: 22000000 INFO @ Wed, 22 Apr 2020 11:01:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:01:57: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:01:57: #1 total tags in treatment: 11083477 INFO @ Wed, 22 Apr 2020 11:01:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:01:57: #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 11:01:57: #1 tags after filtering in treatment: 6074474 INFO @ Wed, 22 Apr 2020 11:01:57: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 11:01:57: #1 finished! INFO @ Wed, 22 Apr 2020 11:01:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:01:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:01:58: 16000000 INFO @ Wed, 22 Apr 2020 11:01:58: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:01:58: Too few paired peaks (0) 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 11:01:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.10_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/SRX7409629/SRX7409629.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:02:02: 17000000 INFO @ Wed, 22 Apr 2020 11:02:07: 18000000 INFO @ Wed, 22 Apr 2020 11:02:11: 19000000 INFO @ Wed, 22 Apr 2020 11:02:16: 20000000 INFO @ Wed, 22 Apr 2020 11:02:20: 21000000 INFO @ Wed, 22 Apr 2020 11:02:25: 22000000 INFO @ Wed, 22 Apr 2020 11:02:27: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:02:27: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:02:27: #1 total tags in treatment: 11083477 INFO @ Wed, 22 Apr 2020 11:02:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:02:27: #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 11:02:27: #1 tags after filtering in treatment: 6074474 INFO @ Wed, 22 Apr 2020 11:02:27: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 11:02:27: #1 finished! INFO @ Wed, 22 Apr 2020 11:02:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:02:27: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 INFO @ Wed, 22 Apr 2020 11:02:28: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:02:28: Too few paired peaks (0) 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 11:02:28: Process for pairing-model is terminated! BigWig に変換中... cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.20_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/SRX7409629/SRX7409629.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409629/SRX7409629.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。