Job ID = 5791205 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:04:13 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 : 13,437,567 reads read : 26,875,134 reads written : 26,875,134 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: 00:11:33 13437567 reads; of these: 13437567 (100.00%) were paired; of these: 3163959 (23.55%) aligned concordantly 0 times 6280156 (46.74%) aligned concordantly exactly 1 time 3993452 (29.72%) aligned concordantly >1 times ---- 3163959 pairs aligned concordantly 0 times; of these: 753361 (23.81%) aligned discordantly 1 time ---- 2410598 pairs aligned 0 times concordantly or discordantly; of these: 4821196 mates make up the pairs; of these: 3810140 (79.03%) aligned 0 times 151669 (3.15%) aligned exactly 1 time 859387 (17.83%) aligned >1 times 85.82% overall alignment rate Time searching: 00:11:33 Overall time: 00:11:33 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 12 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] 3922212 / 10933713 = 0.3587 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 09:33:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.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 09:33:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:33:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:33:45: 1000000 INFO @ Wed, 22 Apr 2020 09:33:51: 2000000 INFO @ Wed, 22 Apr 2020 09:33:57: 3000000 INFO @ Wed, 22 Apr 2020 09:34:03: 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 09:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.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 09:34:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:34:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:34:09: 5000000 INFO @ Wed, 22 Apr 2020 09:34:15: 1000000 INFO @ Wed, 22 Apr 2020 09:34:16: 6000000 INFO @ Wed, 22 Apr 2020 09:34:23: 2000000 INFO @ Wed, 22 Apr 2020 09:34:23: 7000000 INFO @ Wed, 22 Apr 2020 09:34:30: 8000000 INFO @ Wed, 22 Apr 2020 09:34:31: 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 09:34:37: 9000000 INFO @ Wed, 22 Apr 2020 09:34:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.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 09:34:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:34:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:34:39: 4000000 INFO @ Wed, 22 Apr 2020 09:34:44: 10000000 INFO @ Wed, 22 Apr 2020 09:34:46: 1000000 INFO @ Wed, 22 Apr 2020 09:34:47: 5000000 INFO @ Wed, 22 Apr 2020 09:34:51: 11000000 INFO @ Wed, 22 Apr 2020 09:34:53: 2000000 INFO @ Wed, 22 Apr 2020 09:34:55: 6000000 INFO @ Wed, 22 Apr 2020 09:34:58: 12000000 INFO @ Wed, 22 Apr 2020 09:35:00: 3000000 INFO @ Wed, 22 Apr 2020 09:35:03: 7000000 INFO @ Wed, 22 Apr 2020 09:35:05: 13000000 INFO @ Wed, 22 Apr 2020 09:35:08: 4000000 INFO @ Wed, 22 Apr 2020 09:35:12: 8000000 INFO @ Wed, 22 Apr 2020 09:35:12: 14000000 INFO @ Wed, 22 Apr 2020 09:35:16: 5000000 INFO @ Wed, 22 Apr 2020 09:35:19: 15000000 INFO @ Wed, 22 Apr 2020 09:35:20: 9000000 INFO @ Wed, 22 Apr 2020 09:35:21: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:35:21: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:35:21: #1 total tags in treatment: 6462856 INFO @ Wed, 22 Apr 2020 09:35:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:35:21: #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 09:35:21: #1 tags after filtering in treatment: 3707039 INFO @ Wed, 22 Apr 2020 09:35:21: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 09:35:21: #1 finished! INFO @ Wed, 22 Apr 2020 09:35:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:35:21: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 09:35:21: Too few paired peaks (29) 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 09:35:21: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:35:24: 6000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.05_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/SRX6614994/SRX6614994.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:35:27: 10000000 INFO @ Wed, 22 Apr 2020 09:35:31: 7000000 INFO @ Wed, 22 Apr 2020 09:35:35: 11000000 INFO @ Wed, 22 Apr 2020 09:35:38: 8000000 INFO @ Wed, 22 Apr 2020 09:35:43: 12000000 INFO @ Wed, 22 Apr 2020 09:35:45: 9000000 INFO @ Wed, 22 Apr 2020 09:35:51: 13000000 INFO @ Wed, 22 Apr 2020 09:35:51: 10000000 INFO @ Wed, 22 Apr 2020 09:35:58: 11000000 INFO @ Wed, 22 Apr 2020 09:35:58: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:36:05: 12000000 INFO @ Wed, 22 Apr 2020 09:36:06: 15000000 INFO @ Wed, 22 Apr 2020 09:36:07: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:36:07: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:36:07: #1 total tags in treatment: 6462856 INFO @ Wed, 22 Apr 2020 09:36:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:36:07: #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 09:36:08: #1 tags after filtering in treatment: 3707039 INFO @ Wed, 22 Apr 2020 09:36:08: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 09:36:08: #1 finished! INFO @ Wed, 22 Apr 2020 09:36:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:36:08: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 09:36:08: Too few paired peaks (29) 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 09:36:08: Process for pairing-model is terminated! BigWig に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.10_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/SRX6614994/SRX6614994.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:36:12: 13000000 INFO @ Wed, 22 Apr 2020 09:36:18: 14000000 INFO @ Wed, 22 Apr 2020 09:36:25: 15000000 INFO @ Wed, 22 Apr 2020 09:36:26: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:36:26: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:36:26: #1 total tags in treatment: 6462856 INFO @ Wed, 22 Apr 2020 09:36:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:36:26: #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 09:36:26: #1 tags after filtering in treatment: 3707039 INFO @ Wed, 22 Apr 2020 09:36:26: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 09:36:26: #1 finished! INFO @ Wed, 22 Apr 2020 09:36:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:36:26: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 09:36:26: Too few paired peaks (29) 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 09:36:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.20_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/SRX6614994/SRX6614994.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614994/SRX6614994.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling