Job ID = 5721265 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T21:08:29 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 : 18,393,909 reads read : 36,787,818 reads written : 18,393,909 reads 0-length : 18,393,909 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: 00:05:23 18393909 reads; of these: 18393909 (100.00%) were unpaired; of these: 3964994 (21.56%) aligned 0 times 10439906 (56.76%) aligned exactly 1 time 3989009 (21.69%) aligned >1 times 78.44% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 10059003 / 14428915 = 0.6971 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 @ Thu, 16 Apr 2020 06:23:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:23:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:23:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:23:16: 1000000 INFO @ Thu, 16 Apr 2020 06:23:22: 2000000 INFO @ Thu, 16 Apr 2020 06:23:29: 3000000 INFO @ Thu, 16 Apr 2020 06:23:35: 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 @ Thu, 16 Apr 2020 06:23:37: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:23:37: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:23:37: #1 total tags in treatment: 4369912 INFO @ Thu, 16 Apr 2020 06:23:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:23:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:23:37: #1 tags after filtering in treatment: 4369912 INFO @ Thu, 16 Apr 2020 06:23:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:23:37: #1 finished! INFO @ Thu, 16 Apr 2020 06:23:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:23:38: #2 number of paired peaks: 642 WARNING @ Thu, 16 Apr 2020 06:23:38: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Thu, 16 Apr 2020 06:23:38: start model_add_line... INFO @ Thu, 16 Apr 2020 06:23:38: start X-correlation... INFO @ Thu, 16 Apr 2020 06:23:38: end of X-cor INFO @ Thu, 16 Apr 2020 06:23:38: #2 finished! INFO @ Thu, 16 Apr 2020 06:23:38: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 06:23:38: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 16 Apr 2020 06:23:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.05_model.r WARNING @ Thu, 16 Apr 2020 06:23:38: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:23:38: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 16 Apr 2020 06:23:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:23:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:23:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:23:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:23:45: 1000000 INFO @ Thu, 16 Apr 2020 06:23:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:23:52: 2000000 INFO @ Thu, 16 Apr 2020 06:23:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:23:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:23:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.05_summits.bed INFO @ Thu, 16 Apr 2020 06:23:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1357 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:23:58: 3000000 INFO @ Thu, 16 Apr 2020 06:24:04: 4000000 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 @ Thu, 16 Apr 2020 06:24:06: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:24:06: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:24:06: #1 total tags in treatment: 4369912 INFO @ Thu, 16 Apr 2020 06:24:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:24:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:24:06: #1 tags after filtering in treatment: 4369912 INFO @ Thu, 16 Apr 2020 06:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:24:06: #1 finished! INFO @ Thu, 16 Apr 2020 06:24:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:24:07: #2 number of paired peaks: 642 WARNING @ Thu, 16 Apr 2020 06:24:07: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Thu, 16 Apr 2020 06:24:07: start model_add_line... INFO @ Thu, 16 Apr 2020 06:24:07: start X-correlation... INFO @ Thu, 16 Apr 2020 06:24:07: end of X-cor INFO @ Thu, 16 Apr 2020 06:24:07: #2 finished! INFO @ Thu, 16 Apr 2020 06:24:07: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 06:24:07: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 16 Apr 2020 06:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.10_model.r WARNING @ Thu, 16 Apr 2020 06:24:07: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:24:07: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 16 Apr 2020 06:24:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:24:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:24:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 06:24:10: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:24:10: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:24:15: 1000000 INFO @ Thu, 16 Apr 2020 06:24:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:24:20: 2000000 INFO @ Thu, 16 Apr 2020 06:24:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:24:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:24:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.10_summits.bed INFO @ Thu, 16 Apr 2020 06:24:20: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (841 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:24:25: 3000000 INFO @ Thu, 16 Apr 2020 06:24:31: 4000000 INFO @ Thu, 16 Apr 2020 06:24:32: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:24:32: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:24:32: #1 total tags in treatment: 4369912 INFO @ Thu, 16 Apr 2020 06:24:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:24:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:24:33: #1 tags after filtering in treatment: 4369912 INFO @ Thu, 16 Apr 2020 06:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:24:33: #1 finished! INFO @ Thu, 16 Apr 2020 06:24:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:24:33: #2 number of paired peaks: 642 WARNING @ Thu, 16 Apr 2020 06:24:33: Fewer paired peaks (642) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 642 pairs to build model! INFO @ Thu, 16 Apr 2020 06:24:33: start model_add_line... INFO @ Thu, 16 Apr 2020 06:24:33: start X-correlation... INFO @ Thu, 16 Apr 2020 06:24:33: end of X-cor INFO @ Thu, 16 Apr 2020 06:24:33: #2 finished! INFO @ Thu, 16 Apr 2020 06:24:33: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 06:24:33: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 16 Apr 2020 06:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.20_model.r WARNING @ Thu, 16 Apr 2020 06:24:33: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:24:33: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 16 Apr 2020 06:24:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:24:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:24:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277041/SRX7277041.20_summits.bed INFO @ Thu, 16 Apr 2020 06:24:47: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (405 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。