Job ID = 5720964 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:30:43 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 ) 2020-04-15T18:30:43 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 ) 2020-04-15T18:30:43 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 : 43,180,409 reads read : 43,180,409 reads written : 43,180,409 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: 00:10:55 43180409 reads; of these: 43180409 (100.00%) were unpaired; of these: 16726630 (38.74%) aligned 0 times 18300542 (42.38%) aligned exactly 1 time 8153237 (18.88%) aligned >1 times 61.26% overall alignment rate Time searching: 00:10:55 Overall time: 00:10:55 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 12 files... [bam_rmdupse_core] 17773966 / 26453779 = 0.6719 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 04:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.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 04:08:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:08:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:08:07: 1000000 INFO @ Thu, 16 Apr 2020 04:08:13: 2000000 INFO @ Thu, 16 Apr 2020 04:08:19: 3000000 INFO @ Thu, 16 Apr 2020 04:08:25: 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 04:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.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 04:08:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:08:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:08:31: 5000000 INFO @ Thu, 16 Apr 2020 04:08:37: 1000000 INFO @ Thu, 16 Apr 2020 04:08:38: 6000000 INFO @ Thu, 16 Apr 2020 04:08:43: 2000000 INFO @ Thu, 16 Apr 2020 04:08:44: 7000000 INFO @ Thu, 16 Apr 2020 04:08:49: 3000000 INFO @ Thu, 16 Apr 2020 04:08:50: 8000000 INFO @ Thu, 16 Apr 2020 04:08:54: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:08:54: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:08:54: #1 total tags in treatment: 8679813 INFO @ Thu, 16 Apr 2020 04:08:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:08:54: #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 04:08:54: #1 tags after filtering in treatment: 8679813 INFO @ Thu, 16 Apr 2020 04:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:08:54: #1 finished! INFO @ Thu, 16 Apr 2020 04:08:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:08:55: #2 number of paired peaks: 622 WARNING @ Thu, 16 Apr 2020 04:08:55: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Thu, 16 Apr 2020 04:08:55: start model_add_line... INFO @ Thu, 16 Apr 2020 04:08:55: start X-correlation... INFO @ Thu, 16 Apr 2020 04:08:55: end of X-cor INFO @ Thu, 16 Apr 2020 04:08:55: #2 finished! INFO @ Thu, 16 Apr 2020 04:08:55: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 04:08:55: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 04:08:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.05_model.r WARNING @ Thu, 16 Apr 2020 04:08:55: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:08:55: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 04:08:55: #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 04:08:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:08:55: 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 04:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.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 04:09:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:09:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:09:01: 5000000 INFO @ Thu, 16 Apr 2020 04:09:07: 1000000 INFO @ Thu, 16 Apr 2020 04:09:07: 6000000 INFO @ Thu, 16 Apr 2020 04:09:12: 2000000 INFO @ Thu, 16 Apr 2020 04:09:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:09:13: 7000000 INFO @ Thu, 16 Apr 2020 04:09:18: 3000000 INFO @ Thu, 16 Apr 2020 04:09:19: 8000000 INFO @ Thu, 16 Apr 2020 04:09:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:09:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:09:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.05_summits.bed INFO @ Thu, 16 Apr 2020 04:09:21: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2506 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:09:23: 4000000 INFO @ Thu, 16 Apr 2020 04:09:23: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:09:23: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:09:23: #1 total tags in treatment: 8679813 INFO @ Thu, 16 Apr 2020 04:09:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:09:23: #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 04:09:23: #1 tags after filtering in treatment: 8679813 INFO @ Thu, 16 Apr 2020 04:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:09:23: #1 finished! INFO @ Thu, 16 Apr 2020 04:09:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:09:24: #2 number of paired peaks: 622 WARNING @ Thu, 16 Apr 2020 04:09:24: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Thu, 16 Apr 2020 04:09:24: start model_add_line... INFO @ Thu, 16 Apr 2020 04:09:24: start X-correlation... INFO @ Thu, 16 Apr 2020 04:09:24: end of X-cor INFO @ Thu, 16 Apr 2020 04:09:24: #2 finished! INFO @ Thu, 16 Apr 2020 04:09:24: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 04:09:24: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 04:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.10_model.r WARNING @ Thu, 16 Apr 2020 04:09:24: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:09:24: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 04:09:24: #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 04:09:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:09:28: 5000000 INFO @ Thu, 16 Apr 2020 04:09:34: 6000000 INFO @ Thu, 16 Apr 2020 04:09:39: 7000000 INFO @ Thu, 16 Apr 2020 04:09:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:09:44: 8000000 INFO @ Thu, 16 Apr 2020 04:09:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:09:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:09:47: #1 total tags in treatment: 8679813 INFO @ Thu, 16 Apr 2020 04:09:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:09:47: #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 04:09:48: #1 tags after filtering in treatment: 8679813 INFO @ Thu, 16 Apr 2020 04:09:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:09:48: #1 finished! INFO @ Thu, 16 Apr 2020 04:09:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:09:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:09:48: #2 number of paired peaks: 622 WARNING @ Thu, 16 Apr 2020 04:09:48: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Thu, 16 Apr 2020 04:09:48: start model_add_line... INFO @ Thu, 16 Apr 2020 04:09:48: start X-correlation... INFO @ Thu, 16 Apr 2020 04:09:48: end of X-cor INFO @ Thu, 16 Apr 2020 04:09:48: #2 finished! INFO @ Thu, 16 Apr 2020 04:09:48: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 04:09:48: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 04:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.20_model.r WARNING @ Thu, 16 Apr 2020 04:09:48: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:09:48: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 04:09:48: #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 04:09:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:09:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:09:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:09:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:09:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.10_summits.bed INFO @ Thu, 16 Apr 2020 04:09:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1266 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:10:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386757/SRX6386757.20_summits.bed INFO @ Thu, 16 Apr 2020 04:10:16: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (776 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。