Job ID = 5720333 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:36:47 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 : 21,524,298 reads read : 43,048,596 reads written : 21,524,298 reads 0-length : 21,524,298 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: 00:06:36 21524298 reads; of these: 21524298 (100.00%) were unpaired; of these: 1195065 (5.55%) aligned 0 times 17009849 (79.03%) aligned exactly 1 time 3319384 (15.42%) aligned >1 times 94.45% overall alignment rate Time searching: 00:06:36 Overall time: 00:06:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2069504 / 20329233 = 0.1018 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, 15 Apr 2020 23:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.bam'] # control file = None # effective genome size = 9.00e+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, 15 Apr 2020 23:52:12: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:52:12: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:52:19: 1000000 INFO @ Wed, 15 Apr 2020 23:52:25: 2000000 INFO @ Wed, 15 Apr 2020 23:52:32: 3000000 INFO @ Wed, 15 Apr 2020 23:52:39: 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, 15 Apr 2020 23:52:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.bam'] # control file = None # effective genome size = 9.00e+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, 15 Apr 2020 23:52:42: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:52:42: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:52:47: 5000000 INFO @ Wed, 15 Apr 2020 23:52:49: 1000000 INFO @ Wed, 15 Apr 2020 23:52:54: 6000000 INFO @ Wed, 15 Apr 2020 23:52:56: 2000000 INFO @ Wed, 15 Apr 2020 23:53:01: 7000000 INFO @ Wed, 15 Apr 2020 23:53:04: 3000000 INFO @ Wed, 15 Apr 2020 23:53:09: 8000000 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, 15 Apr 2020 23:53:11: 4000000 INFO @ Wed, 15 Apr 2020 23:53:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.bam'] # control file = None # effective genome size = 9.00e+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, 15 Apr 2020 23:53:12: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:53:12: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:53:16: 9000000 INFO @ Wed, 15 Apr 2020 23:53:19: 5000000 INFO @ Wed, 15 Apr 2020 23:53:19: 1000000 INFO @ Wed, 15 Apr 2020 23:53:24: 10000000 INFO @ Wed, 15 Apr 2020 23:53:26: 6000000 INFO @ Wed, 15 Apr 2020 23:53:27: 2000000 INFO @ Wed, 15 Apr 2020 23:53:31: 11000000 INFO @ Wed, 15 Apr 2020 23:53:33: 7000000 INFO @ Wed, 15 Apr 2020 23:53:34: 3000000 INFO @ Wed, 15 Apr 2020 23:53:39: 12000000 INFO @ Wed, 15 Apr 2020 23:53:41: 8000000 INFO @ Wed, 15 Apr 2020 23:53:42: 4000000 INFO @ Wed, 15 Apr 2020 23:53:46: 13000000 INFO @ Wed, 15 Apr 2020 23:53:49: 9000000 INFO @ Wed, 15 Apr 2020 23:53:49: 5000000 INFO @ Wed, 15 Apr 2020 23:53:54: 14000000 INFO @ Wed, 15 Apr 2020 23:53:56: 10000000 INFO @ Wed, 15 Apr 2020 23:53:57: 6000000 INFO @ Wed, 15 Apr 2020 23:54:01: 15000000 INFO @ Wed, 15 Apr 2020 23:54:03: 11000000 INFO @ Wed, 15 Apr 2020 23:54:04: 7000000 INFO @ Wed, 15 Apr 2020 23:54:09: 16000000 INFO @ Wed, 15 Apr 2020 23:54:11: 12000000 INFO @ Wed, 15 Apr 2020 23:54:12: 8000000 INFO @ Wed, 15 Apr 2020 23:54:17: 17000000 INFO @ Wed, 15 Apr 2020 23:54:18: 13000000 INFO @ Wed, 15 Apr 2020 23:54:19: 9000000 INFO @ Wed, 15 Apr 2020 23:54:24: 18000000 INFO @ Wed, 15 Apr 2020 23:54:26: 14000000 INFO @ Wed, 15 Apr 2020 23:54:26: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:54:26: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:54:26: #1 total tags in treatment: 18259729 INFO @ Wed, 15 Apr 2020 23:54:26: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:54:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:54:26: #1 tags after filtering in treatment: 18259729 INFO @ Wed, 15 Apr 2020 23:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:54:26: #1 finished! INFO @ Wed, 15 Apr 2020 23:54:26: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:54:27: 10000000 INFO @ Wed, 15 Apr 2020 23:54:28: #2 number of paired peaks: 225 WARNING @ Wed, 15 Apr 2020 23:54:28: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Wed, 15 Apr 2020 23:54:28: start model_add_line... INFO @ Wed, 15 Apr 2020 23:54:28: start X-correlation... INFO @ Wed, 15 Apr 2020 23:54:28: end of X-cor INFO @ Wed, 15 Apr 2020 23:54:28: #2 finished! INFO @ Wed, 15 Apr 2020 23:54:28: #2 predicted fragment length is 73 bps INFO @ Wed, 15 Apr 2020 23:54:28: #2 alternative fragment length(s) may be 2,55,73 bps INFO @ Wed, 15 Apr 2020 23:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.05_model.r WARNING @ Wed, 15 Apr 2020 23:54:28: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:54:28: #2 You may need to consider one of the other alternative d(s): 2,55,73 WARNING @ Wed, 15 Apr 2020 23:54:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:54:28: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:54:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:54:33: 15000000 INFO @ Wed, 15 Apr 2020 23:54:34: 11000000 INFO @ Wed, 15 Apr 2020 23:54:40: 16000000 INFO @ Wed, 15 Apr 2020 23:54:42: 12000000 INFO @ Wed, 15 Apr 2020 23:54:48: 17000000 INFO @ Wed, 15 Apr 2020 23:54:49: 13000000 INFO @ Wed, 15 Apr 2020 23:54:55: 18000000 INFO @ Wed, 15 Apr 2020 23:54:57: 14000000 INFO @ Wed, 15 Apr 2020 23:54:57: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:54:57: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:54:57: #1 total tags in treatment: 18259729 INFO @ Wed, 15 Apr 2020 23:54:57: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:54:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:54:58: #1 tags after filtering in treatment: 18259729 INFO @ Wed, 15 Apr 2020 23:54:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:54:58: #1 finished! INFO @ Wed, 15 Apr 2020 23:54:58: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:54:59: #2 number of paired peaks: 225 WARNING @ Wed, 15 Apr 2020 23:54:59: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Wed, 15 Apr 2020 23:54:59: start model_add_line... INFO @ Wed, 15 Apr 2020 23:54:59: start X-correlation... INFO @ Wed, 15 Apr 2020 23:54:59: end of X-cor INFO @ Wed, 15 Apr 2020 23:54:59: #2 finished! INFO @ Wed, 15 Apr 2020 23:54:59: #2 predicted fragment length is 73 bps INFO @ Wed, 15 Apr 2020 23:54:59: #2 alternative fragment length(s) may be 2,55,73 bps INFO @ Wed, 15 Apr 2020 23:54:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.10_model.r WARNING @ Wed, 15 Apr 2020 23:54:59: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:54:59: #2 You may need to consider one of the other alternative d(s): 2,55,73 WARNING @ Wed, 15 Apr 2020 23:54:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:54:59: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:55:00: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:55:04: 15000000 INFO @ Wed, 15 Apr 2020 23:55:11: 16000000 INFO @ Wed, 15 Apr 2020 23:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.05_summits.bed INFO @ Wed, 15 Apr 2020 23:55:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (624 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:55:18: 17000000 INFO @ Wed, 15 Apr 2020 23:55:25: 18000000 INFO @ Wed, 15 Apr 2020 23:55:27: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:55:27: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:55:27: #1 total tags in treatment: 18259729 INFO @ Wed, 15 Apr 2020 23:55:27: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:55:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:55:27: #1 tags after filtering in treatment: 18259729 INFO @ Wed, 15 Apr 2020 23:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:55:27: #1 finished! INFO @ Wed, 15 Apr 2020 23:55:27: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:55:28: #2 number of paired peaks: 225 WARNING @ Wed, 15 Apr 2020 23:55:28: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Wed, 15 Apr 2020 23:55:28: start model_add_line... INFO @ Wed, 15 Apr 2020 23:55:28: start X-correlation... INFO @ Wed, 15 Apr 2020 23:55:28: end of X-cor INFO @ Wed, 15 Apr 2020 23:55:28: #2 finished! INFO @ Wed, 15 Apr 2020 23:55:28: #2 predicted fragment length is 73 bps INFO @ Wed, 15 Apr 2020 23:55:28: #2 alternative fragment length(s) may be 2,55,73 bps INFO @ Wed, 15 Apr 2020 23:55:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.20_model.r WARNING @ Wed, 15 Apr 2020 23:55:28: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:55:28: #2 You may need to consider one of the other alternative d(s): 2,55,73 WARNING @ Wed, 15 Apr 2020 23:55:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:55:28: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:55:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:55:31: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:55:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:55:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:55:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.10_summits.bed INFO @ Wed, 15 Apr 2020 23:55:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (451 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:55:59: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:56:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:56:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:56:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971799/SRX7971799.20_summits.bed INFO @ Wed, 15 Apr 2020 23:56:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。