Job ID = 5791163 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:39:22 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 ) 2020-04-21T23:47:32 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 ) 2020-04-21T23:47:32 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 : 12,832,074 reads read : 25,664,148 reads written : 25,664,148 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: 00:14:21 12832074 reads; of these: 12832074 (100.00%) were paired; of these: 6991243 (54.48%) aligned concordantly 0 times 4749757 (37.01%) aligned concordantly exactly 1 time 1091074 (8.50%) aligned concordantly >1 times ---- 6991243 pairs aligned concordantly 0 times; of these: 2743572 (39.24%) aligned discordantly 1 time ---- 4247671 pairs aligned 0 times concordantly or discordantly; of these: 8495342 mates make up the pairs; of these: 7054780 (83.04%) aligned 0 times 225199 (2.65%) aligned exactly 1 time 1215363 (14.31%) aligned >1 times 72.51% overall alignment rate Time searching: 00:14:21 Overall time: 00:14:21 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] 1721820 / 8417745 = 0.2045 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 09:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.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 09:24:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:24:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:24:49: 1000000 INFO @ Wed, 22 Apr 2020 09:24:56: 2000000 INFO @ Wed, 22 Apr 2020 09:25:04: 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 09:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.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 09:25:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:25:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:25:12: 4000000 INFO @ Wed, 22 Apr 2020 09:25:18: 1000000 INFO @ Wed, 22 Apr 2020 09:25:21: 5000000 INFO @ Wed, 22 Apr 2020 09:25:28: 2000000 INFO @ Wed, 22 Apr 2020 09:25:31: 6000000 INFO @ Wed, 22 Apr 2020 09:25:37: 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 09:25:40: 7000000 INFO @ Wed, 22 Apr 2020 09:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.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 09:25:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:25:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:25:46: 4000000 INFO @ Wed, 22 Apr 2020 09:25:49: 8000000 INFO @ Wed, 22 Apr 2020 09:25:50: 1000000 INFO @ Wed, 22 Apr 2020 09:25:55: 5000000 INFO @ Wed, 22 Apr 2020 09:25:59: 9000000 INFO @ Wed, 22 Apr 2020 09:25:59: 2000000 INFO @ Wed, 22 Apr 2020 09:26:05: 6000000 INFO @ Wed, 22 Apr 2020 09:26:08: 10000000 INFO @ Wed, 22 Apr 2020 09:26:09: 3000000 INFO @ Wed, 22 Apr 2020 09:26:14: 7000000 INFO @ Wed, 22 Apr 2020 09:26:17: 11000000 INFO @ Wed, 22 Apr 2020 09:26:18: 4000000 INFO @ Wed, 22 Apr 2020 09:26:23: 8000000 INFO @ Wed, 22 Apr 2020 09:26:26: 12000000 INFO @ Wed, 22 Apr 2020 09:26:27: 5000000 INFO @ Wed, 22 Apr 2020 09:26:33: 9000000 INFO @ Wed, 22 Apr 2020 09:26:36: 13000000 INFO @ Wed, 22 Apr 2020 09:26:37: 6000000 INFO @ Wed, 22 Apr 2020 09:26:42: 10000000 INFO @ Wed, 22 Apr 2020 09:26:45: 14000000 INFO @ Wed, 22 Apr 2020 09:26:46: 7000000 INFO @ Wed, 22 Apr 2020 09:26:51: 11000000 INFO @ Wed, 22 Apr 2020 09:26:54: 15000000 INFO @ Wed, 22 Apr 2020 09:26:55: 8000000 INFO @ Wed, 22 Apr 2020 09:26:56: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:26:56: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:26:56: #1 total tags in treatment: 4564575 INFO @ Wed, 22 Apr 2020 09:26:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:26:56: #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 09:26:56: #1 tags after filtering in treatment: 3047713 INFO @ Wed, 22 Apr 2020 09:26:56: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:26:56: #1 finished! INFO @ Wed, 22 Apr 2020 09:26:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:26:56: #2 number of paired peaks: 19 WARNING @ Wed, 22 Apr 2020 09:26:56: Too few paired peaks (19) 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 09:26:56: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:27:01: 12000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.05_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/SRX6614957/SRX6614957.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:27:04: 9000000 INFO @ Wed, 22 Apr 2020 09:27:10: 13000000 INFO @ Wed, 22 Apr 2020 09:27:13: 10000000 INFO @ Wed, 22 Apr 2020 09:27:19: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:27:23: 11000000 INFO @ Wed, 22 Apr 2020 09:27:29: 15000000 INFO @ Wed, 22 Apr 2020 09:27:30: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:27:30: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:27:30: #1 total tags in treatment: 4564575 INFO @ Wed, 22 Apr 2020 09:27:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:27:30: #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 09:27:30: #1 tags after filtering in treatment: 3047713 INFO @ Wed, 22 Apr 2020 09:27:30: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:27:30: #1 finished! INFO @ Wed, 22 Apr 2020 09:27:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:27:30: #2 number of paired peaks: 19 WARNING @ Wed, 22 Apr 2020 09:27:30: Too few paired peaks (19) 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 09:27:30: Process for pairing-model is terminated! BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:27:32: 12000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.10_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/SRX6614957/SRX6614957.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:27:41: 13000000 INFO @ Wed, 22 Apr 2020 09:27:50: 14000000 INFO @ Wed, 22 Apr 2020 09:27:59: 15000000 INFO @ Wed, 22 Apr 2020 09:28:00: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:28:00: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:28:00: #1 total tags in treatment: 4564575 INFO @ Wed, 22 Apr 2020 09:28:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:28:00: #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 09:28:01: #1 tags after filtering in treatment: 3047713 INFO @ Wed, 22 Apr 2020 09:28:01: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 09:28:01: #1 finished! INFO @ Wed, 22 Apr 2020 09:28:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:28:01: #2 number of paired peaks: 19 WARNING @ Wed, 22 Apr 2020 09:28:01: Too few paired peaks (19) 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 09:28:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.20_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/SRX6614957/SRX6614957.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614957/SRX6614957.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling