Job ID = 5791650 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:16:09 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 : 20,583,547 reads read : 41,167,094 reads written : 41,167,094 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: 00:11:30 20583547 reads; of these: 20583547 (100.00%) were paired; of these: 643048 (3.12%) aligned concordantly 0 times 17861468 (86.78%) aligned concordantly exactly 1 time 2079031 (10.10%) aligned concordantly >1 times ---- 643048 pairs aligned concordantly 0 times; of these: 29815 (4.64%) aligned discordantly 1 time ---- 613233 pairs aligned 0 times concordantly or discordantly; of these: 1226466 mates make up the pairs; of these: 1013434 (82.63%) aligned 0 times 178205 (14.53%) aligned exactly 1 time 34827 (2.84%) aligned >1 times 97.54% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 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 20 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] 2557892 / 19946502 = 0.1282 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 10:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.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 10:38:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:38:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:38:40: 1000000 INFO @ Wed, 22 Apr 2020 10:38:46: 2000000 INFO @ Wed, 22 Apr 2020 10:38:51: 3000000 INFO @ Wed, 22 Apr 2020 10:38:57: 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 10:39:03: 5000000 INFO @ Wed, 22 Apr 2020 10:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.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 10:39:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:39:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:39:10: 6000000 INFO @ Wed, 22 Apr 2020 10:39:11: 1000000 INFO @ Wed, 22 Apr 2020 10:39:17: 2000000 INFO @ Wed, 22 Apr 2020 10:39:17: 7000000 INFO @ Wed, 22 Apr 2020 10:39:23: 3000000 INFO @ Wed, 22 Apr 2020 10:39:24: 8000000 INFO @ Wed, 22 Apr 2020 10:39:29: 4000000 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 10:39:32: 9000000 INFO @ Wed, 22 Apr 2020 10:39:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.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 10:39:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:39:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:39:35: 5000000 INFO @ Wed, 22 Apr 2020 10:39:39: 10000000 INFO @ Wed, 22 Apr 2020 10:39:41: 6000000 INFO @ Wed, 22 Apr 2020 10:39:42: 1000000 INFO @ Wed, 22 Apr 2020 10:39:46: 11000000 INFO @ Wed, 22 Apr 2020 10:39:48: 7000000 INFO @ Wed, 22 Apr 2020 10:39:49: 2000000 INFO @ Wed, 22 Apr 2020 10:39:53: 12000000 INFO @ Wed, 22 Apr 2020 10:39:54: 8000000 INFO @ Wed, 22 Apr 2020 10:39:56: 3000000 INFO @ Wed, 22 Apr 2020 10:40:00: 9000000 INFO @ Wed, 22 Apr 2020 10:40:01: 13000000 INFO @ Wed, 22 Apr 2020 10:40:04: 4000000 INFO @ Wed, 22 Apr 2020 10:40:06: 10000000 INFO @ Wed, 22 Apr 2020 10:40:08: 14000000 INFO @ Wed, 22 Apr 2020 10:40:11: 5000000 INFO @ Wed, 22 Apr 2020 10:40:13: 11000000 INFO @ Wed, 22 Apr 2020 10:40:15: 15000000 INFO @ Wed, 22 Apr 2020 10:40:18: 6000000 INFO @ Wed, 22 Apr 2020 10:40:20: 12000000 INFO @ Wed, 22 Apr 2020 10:40:23: 16000000 INFO @ Wed, 22 Apr 2020 10:40:26: 7000000 INFO @ Wed, 22 Apr 2020 10:40:26: 13000000 INFO @ Wed, 22 Apr 2020 10:40:30: 17000000 INFO @ Wed, 22 Apr 2020 10:40:32: 14000000 INFO @ Wed, 22 Apr 2020 10:40:33: 8000000 INFO @ Wed, 22 Apr 2020 10:40:37: 18000000 INFO @ Wed, 22 Apr 2020 10:40:39: 15000000 INFO @ Wed, 22 Apr 2020 10:40:40: 9000000 INFO @ Wed, 22 Apr 2020 10:40:45: 19000000 INFO @ Wed, 22 Apr 2020 10:40:45: 16000000 INFO @ Wed, 22 Apr 2020 10:40:47: 10000000 INFO @ Wed, 22 Apr 2020 10:40:51: 17000000 INFO @ Wed, 22 Apr 2020 10:40:52: 20000000 INFO @ Wed, 22 Apr 2020 10:40:55: 11000000 INFO @ Wed, 22 Apr 2020 10:40:57: 18000000 INFO @ Wed, 22 Apr 2020 10:40:59: 21000000 INFO @ Wed, 22 Apr 2020 10:41:02: 12000000 INFO @ Wed, 22 Apr 2020 10:41:04: 19000000 INFO @ Wed, 22 Apr 2020 10:41:06: 22000000 INFO @ Wed, 22 Apr 2020 10:41:09: 13000000 INFO @ Wed, 22 Apr 2020 10:41:10: 20000000 INFO @ Wed, 22 Apr 2020 10:41:13: 23000000 INFO @ Wed, 22 Apr 2020 10:41:16: 21000000 INFO @ Wed, 22 Apr 2020 10:41:16: 14000000 INFO @ Wed, 22 Apr 2020 10:41:21: 24000000 INFO @ Wed, 22 Apr 2020 10:41:22: 22000000 INFO @ Wed, 22 Apr 2020 10:41:23: 15000000 INFO @ Wed, 22 Apr 2020 10:41:28: 25000000 INFO @ Wed, 22 Apr 2020 10:41:28: 23000000 INFO @ Wed, 22 Apr 2020 10:41:31: 16000000 INFO @ Wed, 22 Apr 2020 10:41:34: 24000000 INFO @ Wed, 22 Apr 2020 10:41:35: 26000000 INFO @ Wed, 22 Apr 2020 10:41:38: 17000000 INFO @ Wed, 22 Apr 2020 10:41:41: 25000000 INFO @ Wed, 22 Apr 2020 10:41:42: 27000000 INFO @ Wed, 22 Apr 2020 10:41:45: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:41:47: 26000000 INFO @ Wed, 22 Apr 2020 10:41:50: 28000000 INFO @ Wed, 22 Apr 2020 10:41:53: 19000000 INFO @ Wed, 22 Apr 2020 10:41:53: 27000000 INFO @ Wed, 22 Apr 2020 10:41:57: 29000000 INFO @ Wed, 22 Apr 2020 10:41:59: 28000000 INFO @ Wed, 22 Apr 2020 10:42:00: 20000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:42:04: 30000000 INFO @ Wed, 22 Apr 2020 10:42:05: 29000000 INFO @ Wed, 22 Apr 2020 10:42:07: 21000000 INFO @ Wed, 22 Apr 2020 10:42:11: 31000000 INFO @ Wed, 22 Apr 2020 10:42:12: 30000000 INFO @ Wed, 22 Apr 2020 10:42:14: 22000000 INFO @ Wed, 22 Apr 2020 10:42:18: 32000000 INFO @ Wed, 22 Apr 2020 10:42:18: 31000000 INFO @ Wed, 22 Apr 2020 10:42:21: 23000000 INFO @ Wed, 22 Apr 2020 10:42:24: 33000000 INFO @ Wed, 22 Apr 2020 10:42:25: 32000000 INFO @ Wed, 22 Apr 2020 10:42:28: 24000000 INFO @ Wed, 22 Apr 2020 10:42:30: 34000000 INFO @ Wed, 22 Apr 2020 10:42:32: 33000000 INFO @ Wed, 22 Apr 2020 10:42:36: 25000000 INFO @ Wed, 22 Apr 2020 10:42:36: 35000000 INFO @ Wed, 22 Apr 2020 10:42:37: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:42:37: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:42:37: #1 total tags in treatment: 17383435 INFO @ Wed, 22 Apr 2020 10:42:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:42:37: #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 10:42:37: #1 tags after filtering in treatment: 10372209 INFO @ Wed, 22 Apr 2020 10:42:37: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:42:37: #1 finished! INFO @ Wed, 22 Apr 2020 10:42:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:42:38: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:42:38: 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 10:42:38: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:42:39: 34000000 INFO @ Wed, 22 Apr 2020 10:42:43: 26000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.05_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/SRX7409614/SRX7409614.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:42:46: 35000000 INFO @ Wed, 22 Apr 2020 10:42:47: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:42:47: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:42:47: #1 total tags in treatment: 17383435 INFO @ Wed, 22 Apr 2020 10:42:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:42:47: #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 10:42:47: #1 tags after filtering in treatment: 10372209 INFO @ Wed, 22 Apr 2020 10:42:47: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:42:47: #1 finished! INFO @ Wed, 22 Apr 2020 10:42:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:42:48: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:42:48: 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 10:42:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.10_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/SRX7409614/SRX7409614.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:42:50: 27000000 INFO @ Wed, 22 Apr 2020 10:42:56: 28000000 INFO @ Wed, 22 Apr 2020 10:43:03: 29000000 INFO @ Wed, 22 Apr 2020 10:43:10: 30000000 INFO @ Wed, 22 Apr 2020 10:43:16: 31000000 INFO @ Wed, 22 Apr 2020 10:43:21: 32000000 INFO @ Wed, 22 Apr 2020 10:43:27: 33000000 INFO @ Wed, 22 Apr 2020 10:43:32: 34000000 INFO @ Wed, 22 Apr 2020 10:43:37: 35000000 INFO @ Wed, 22 Apr 2020 10:43:37: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:43:37: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:43:37: #1 total tags in treatment: 17383435 INFO @ Wed, 22 Apr 2020 10:43:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:43:37: #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 10:43:38: #1 tags after filtering in treatment: 10372209 INFO @ Wed, 22 Apr 2020 10:43:38: #1 Redundant rate of treatment: 0.40 INFO @ Wed, 22 Apr 2020 10:43:38: #1 finished! INFO @ Wed, 22 Apr 2020 10:43:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:43:38: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:43:38: 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 10:43:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.20_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/SRX7409614/SRX7409614.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409614/SRX7409614.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling