Job ID = 5791815 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:43:23 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 : 10,886,713 reads read : 21,773,426 reads written : 21,773,426 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: 00:10:07 10886713 reads; of these: 10886713 (100.00%) were paired; of these: 2561165 (23.53%) aligned concordantly 0 times 7254655 (66.64%) aligned concordantly exactly 1 time 1070893 (9.84%) aligned concordantly >1 times ---- 2561165 pairs aligned concordantly 0 times; of these: 804670 (31.42%) aligned discordantly 1 time ---- 1756495 pairs aligned 0 times concordantly or discordantly; of these: 3512990 mates make up the pairs; of these: 3063400 (87.20%) aligned 0 times 195882 (5.58%) aligned exactly 1 time 253708 (7.22%) aligned >1 times 85.93% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 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] 1381366 / 9070402 = 0.1523 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 11:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.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 11:09:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:09:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:09:51: 1000000 INFO @ Wed, 22 Apr 2020 11:09:57: 2000000 INFO @ Wed, 22 Apr 2020 11:10:05: 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 11:10:12: 4000000 INFO @ Wed, 22 Apr 2020 11:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.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 11:10:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:10:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:10:20: 1000000 INFO @ Wed, 22 Apr 2020 11:10:20: 5000000 INFO @ Wed, 22 Apr 2020 11:10:27: 6000000 INFO @ Wed, 22 Apr 2020 11:10:27: 2000000 INFO @ Wed, 22 Apr 2020 11:10:34: 7000000 INFO @ Wed, 22 Apr 2020 11:10:34: 3000000 BedGraph に変換中... INFO @ Wed, 22 Apr 2020 11:10:40: 8000000 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 11:10:42: 4000000 INFO @ Wed, 22 Apr 2020 11:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.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 11:10:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:10:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:10:47: 9000000 INFO @ Wed, 22 Apr 2020 11:10:49: 5000000 INFO @ Wed, 22 Apr 2020 11:10:50: 1000000 INFO @ Wed, 22 Apr 2020 11:10:55: 10000000 INFO @ Wed, 22 Apr 2020 11:10:57: 6000000 INFO @ Wed, 22 Apr 2020 11:10:58: 2000000 INFO @ Wed, 22 Apr 2020 11:11:02: 11000000 INFO @ Wed, 22 Apr 2020 11:11:04: 7000000 INFO @ Wed, 22 Apr 2020 11:11:07: 3000000 INFO @ Wed, 22 Apr 2020 11:11:12: 12000000 INFO @ Wed, 22 Apr 2020 11:11:12: 8000000 INFO @ Wed, 22 Apr 2020 11:11:15: 4000000 INFO @ Wed, 22 Apr 2020 11:11:19: 13000000 INFO @ Wed, 22 Apr 2020 11:11:19: 9000000 INFO @ Wed, 22 Apr 2020 11:11:22: 5000000 INFO @ Wed, 22 Apr 2020 11:11:25: 14000000 INFO @ Wed, 22 Apr 2020 11:11:27: 10000000 INFO @ Wed, 22 Apr 2020 11:11:29: 6000000 INFO @ Wed, 22 Apr 2020 11:11:32: 15000000 INFO @ Wed, 22 Apr 2020 11:11:35: 11000000 INFO @ Wed, 22 Apr 2020 11:11:36: 7000000 INFO @ Wed, 22 Apr 2020 11:11:39: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:11:39: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:11:39: #1 total tags in treatment: 7055825 INFO @ Wed, 22 Apr 2020 11:11:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:11:39: #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 11:11:39: #1 tags after filtering in treatment: 3717421 INFO @ Wed, 22 Apr 2020 11:11:39: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 22 Apr 2020 11:11:39: #1 finished! INFO @ Wed, 22 Apr 2020 11:11:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:11:39: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:11:39: 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 11:11:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.05_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/SRX7756599/SRX7756599.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:11:43: 8000000 INFO @ Wed, 22 Apr 2020 11:11:44: 12000000 INFO @ Wed, 22 Apr 2020 11:11:50: 9000000 INFO @ Wed, 22 Apr 2020 11:11:51: 13000000 INFO @ Wed, 22 Apr 2020 11:11:56: 10000000 INFO @ Wed, 22 Apr 2020 11:11:58: 14000000 INFO @ Wed, 22 Apr 2020 11:12:04: 11000000 INFO @ Wed, 22 Apr 2020 11:12:05: 15000000 INFO @ Wed, 22 Apr 2020 11:12:11: 12000000 INFO @ Wed, 22 Apr 2020 11:12:12: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:12:12: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:12:12: #1 total tags in treatment: 7055825 INFO @ Wed, 22 Apr 2020 11:12:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:12:12: #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 11:12:12: #1 tags after filtering in treatment: 3717421 INFO @ Wed, 22 Apr 2020 11:12:12: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 22 Apr 2020 11:12:12: #1 finished! INFO @ Wed, 22 Apr 2020 11:12:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:12:13: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:12:13: 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 11:12:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:12:17: 13000000 INFO @ Wed, 22 Apr 2020 11:12:23: 14000000 INFO @ Wed, 22 Apr 2020 11:12:30: 15000000 INFO @ Wed, 22 Apr 2020 11:12:37: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:12:37: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:12:37: #1 total tags in treatment: 7055825 INFO @ Wed, 22 Apr 2020 11:12:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:12:37: #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 11:12:37: #1 tags after filtering in treatment: 3717421 INFO @ Wed, 22 Apr 2020 11:12:37: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 22 Apr 2020 11:12:37: #1 finished! INFO @ Wed, 22 Apr 2020 11:12:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:12:37: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:12:37: 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 11:12:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.20_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/SRX7756599/SRX7756599.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756599/SRX7756599.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。