Job ID = 5720305 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T13:59:42 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 ) 2020-04-15T13:59:42 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 : 3,682,205 reads read : 3,682,205 reads written : 3,682,205 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: 00:00:42 3682205 reads; of these: 3682205 (100.00%) were unpaired; of these: 378433 (10.28%) aligned 0 times 2691065 (73.08%) aligned exactly 1 time 612707 (16.64%) aligned >1 times 89.72% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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_rmdupse_core] 2212874 / 3303772 = 0.6698 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 23:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.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 23:03:33: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:03:33: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:03:38: 1000000 INFO @ Wed, 15 Apr 2020 23:03:38: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:03:38: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:03:38: #1 total tags in treatment: 1090898 INFO @ Wed, 15 Apr 2020 23:03:38: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:03:38: #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 23:03:38: #1 tags after filtering in treatment: 1090898 INFO @ Wed, 15 Apr 2020 23:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:03:38: #1 finished! INFO @ Wed, 15 Apr 2020 23:03:38: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:03:38: #2 number of paired peaks: 849 WARNING @ Wed, 15 Apr 2020 23:03:38: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Wed, 15 Apr 2020 23:03:38: start model_add_line... INFO @ Wed, 15 Apr 2020 23:03:38: start X-correlation... INFO @ Wed, 15 Apr 2020 23:03:38: end of X-cor INFO @ Wed, 15 Apr 2020 23:03:38: #2 finished! INFO @ Wed, 15 Apr 2020 23:03:38: #2 predicted fragment length is 53 bps INFO @ Wed, 15 Apr 2020 23:03:38: #2 alternative fragment length(s) may be 53,539 bps INFO @ Wed, 15 Apr 2020 23:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.05_model.r WARNING @ Wed, 15 Apr 2020 23:03:38: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:03:38: #2 You may need to consider one of the other alternative d(s): 53,539 WARNING @ Wed, 15 Apr 2020 23:03:38: #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 23:03:38: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:03:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:03:41: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.05_summits.bed INFO @ Wed, 15 Apr 2020 23:03:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (470 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 23:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.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 23:04:02: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:04:02: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:04:07: 1000000 INFO @ Wed, 15 Apr 2020 23:04:08: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:04:08: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:04:08: #1 total tags in treatment: 1090898 INFO @ Wed, 15 Apr 2020 23:04:08: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:04:08: #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 23:04:08: #1 tags after filtering in treatment: 1090898 INFO @ Wed, 15 Apr 2020 23:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:04:08: #1 finished! INFO @ Wed, 15 Apr 2020 23:04:08: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:04:08: #2 number of paired peaks: 849 WARNING @ Wed, 15 Apr 2020 23:04:08: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Wed, 15 Apr 2020 23:04:08: start model_add_line... INFO @ Wed, 15 Apr 2020 23:04:08: start X-correlation... INFO @ Wed, 15 Apr 2020 23:04:08: end of X-cor INFO @ Wed, 15 Apr 2020 23:04:08: #2 finished! INFO @ Wed, 15 Apr 2020 23:04:08: #2 predicted fragment length is 53 bps INFO @ Wed, 15 Apr 2020 23:04:08: #2 alternative fragment length(s) may be 53,539 bps INFO @ Wed, 15 Apr 2020 23:04:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.10_model.r WARNING @ Wed, 15 Apr 2020 23:04:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:04:08: #2 You may need to consider one of the other alternative d(s): 53,539 WARNING @ Wed, 15 Apr 2020 23:04:08: #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 23:04:08: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:04:10: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.10_summits.bed INFO @ Wed, 15 Apr 2020 23:04:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (238 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 23:04:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.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 23:04:31: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:04:31: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:04:36: 1000000 INFO @ Wed, 15 Apr 2020 23:04:37: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:04:37: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:04:37: #1 total tags in treatment: 1090898 INFO @ Wed, 15 Apr 2020 23:04:37: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:04:37: #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 23:04:37: #1 tags after filtering in treatment: 1090898 INFO @ Wed, 15 Apr 2020 23:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:04:37: #1 finished! INFO @ Wed, 15 Apr 2020 23:04:37: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:04:37: #2 number of paired peaks: 849 WARNING @ Wed, 15 Apr 2020 23:04:37: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Wed, 15 Apr 2020 23:04:37: start model_add_line... INFO @ Wed, 15 Apr 2020 23:04:37: start X-correlation... INFO @ Wed, 15 Apr 2020 23:04:37: end of X-cor INFO @ Wed, 15 Apr 2020 23:04:37: #2 finished! INFO @ Wed, 15 Apr 2020 23:04:37: #2 predicted fragment length is 53 bps INFO @ Wed, 15 Apr 2020 23:04:37: #2 alternative fragment length(s) may be 53,539 bps INFO @ Wed, 15 Apr 2020 23:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.20_model.r WARNING @ Wed, 15 Apr 2020 23:04:37: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:04:37: #2 You may need to consider one of the other alternative d(s): 53,539 WARNING @ Wed, 15 Apr 2020 23:04:37: #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 23:04:37: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:04:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 15 Apr 2020 23:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627553/SRX7627553.20_summits.bed INFO @ Wed, 15 Apr 2020 23:04:40: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (88 records, 4 fields): 1 millis CompletedMACS2peakCalling