Job ID = 5791276 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:22:34 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 : 13,053,528 reads read : 26,107,056 reads written : 26,107,056 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: 00:03:54 13053528 reads; of these: 13053528 (100.00%) were paired; of these: 7976829 (61.11%) aligned concordantly 0 times 3932177 (30.12%) aligned concordantly exactly 1 time 1144522 (8.77%) aligned concordantly >1 times ---- 7976829 pairs aligned concordantly 0 times; of these: 673929 (8.45%) aligned discordantly 1 time ---- 7302900 pairs aligned 0 times concordantly or discordantly; of these: 14605800 mates make up the pairs; of these: 12632037 (86.49%) aligned 0 times 1406694 (9.63%) aligned exactly 1 time 567069 (3.88%) aligned >1 times 51.61% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 1823416 / 5603794 = 0.3254 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 09:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.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 09:33:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:33:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:33:58: 1000000 INFO @ Wed, 22 Apr 2020 09:34:02: 2000000 INFO @ Wed, 22 Apr 2020 09:34:06: 3000000 INFO @ Wed, 22 Apr 2020 09:34:10: 4000000 INFO @ Wed, 22 Apr 2020 09:34:14: 5000000 INFO @ Wed, 22 Apr 2020 09:34:18: 6000000 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 09:34:23: 7000000 INFO @ Wed, 22 Apr 2020 09:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.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 09:34:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:34:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:34:27: 8000000 INFO @ Wed, 22 Apr 2020 09:34:28: 1000000 INFO @ Wed, 22 Apr 2020 09:34:32: 9000000 INFO @ Wed, 22 Apr 2020 09:34:33: 2000000 INFO @ Wed, 22 Apr 2020 09:34:35: #1 tag size is determined as 40 bps INFO @ Wed, 22 Apr 2020 09:34:35: #1 tag size = 40 INFO @ Wed, 22 Apr 2020 09:34:35: #1 total tags in treatment: 3478911 INFO @ Wed, 22 Apr 2020 09:34:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:34:35: #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 09:34:35: #1 tags after filtering in treatment: 2297554 INFO @ Wed, 22 Apr 2020 09:34:35: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:34:35: #1 finished! INFO @ Wed, 22 Apr 2020 09:34:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:34:36: #2 number of paired peaks: 40 WARNING @ Wed, 22 Apr 2020 09:34:36: Too few paired peaks (40) 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 09:34:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.05_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/SRX7399907/SRX7399907.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:34:37: 3000000 INFO @ Wed, 22 Apr 2020 09:34:41: 4000000 INFO @ Wed, 22 Apr 2020 09:34:46: 5000000 INFO @ Wed, 22 Apr 2020 09:34:50: 6000000 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 09:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.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 09:34:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:34:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:34:54: 7000000 INFO @ Wed, 22 Apr 2020 09:34:58: 1000000 INFO @ Wed, 22 Apr 2020 09:34:59: 8000000 INFO @ Wed, 22 Apr 2020 09:35:03: 2000000 INFO @ Wed, 22 Apr 2020 09:35:03: 9000000 INFO @ Wed, 22 Apr 2020 09:35:07: 3000000 INFO @ Wed, 22 Apr 2020 09:35:07: #1 tag size is determined as 40 bps INFO @ Wed, 22 Apr 2020 09:35:07: #1 tag size = 40 INFO @ Wed, 22 Apr 2020 09:35:07: #1 total tags in treatment: 3478911 INFO @ Wed, 22 Apr 2020 09:35:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:35:07: #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 09:35:07: #1 tags after filtering in treatment: 2297554 INFO @ Wed, 22 Apr 2020 09:35:07: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:35:07: #1 finished! INFO @ Wed, 22 Apr 2020 09:35:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:35:07: #2 number of paired peaks: 40 WARNING @ Wed, 22 Apr 2020 09:35:07: Too few paired peaks (40) 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 09:35:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.10_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/SRX7399907/SRX7399907.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:35:11: 4000000 INFO @ Wed, 22 Apr 2020 09:35:16: 5000000 INFO @ Wed, 22 Apr 2020 09:35:20: 6000000 INFO @ Wed, 22 Apr 2020 09:35:24: 7000000 INFO @ Wed, 22 Apr 2020 09:35:28: 8000000 INFO @ Wed, 22 Apr 2020 09:35:33: 9000000 INFO @ Wed, 22 Apr 2020 09:35:36: #1 tag size is determined as 40 bps INFO @ Wed, 22 Apr 2020 09:35:36: #1 tag size = 40 INFO @ Wed, 22 Apr 2020 09:35:36: #1 total tags in treatment: 3478911 INFO @ Wed, 22 Apr 2020 09:35:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:35:36: #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 09:35:36: #1 tags after filtering in treatment: 2297554 INFO @ Wed, 22 Apr 2020 09:35:36: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:35:36: #1 finished! INFO @ Wed, 22 Apr 2020 09:35:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:35:37: #2 number of paired peaks: 40 WARNING @ Wed, 22 Apr 2020 09:35:37: Too few paired peaks (40) 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 09:35:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.20_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/SRX7399907/SRX7399907.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399907/SRX7399907.20_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。