Job ID = 5720905 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:07:22 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 : 17,957,873 reads read : 17,957,873 reads written : 17,957,873 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: 00:07:43 17957873 reads; of these: 17957873 (100.00%) were unpaired; of these: 724170 (4.03%) aligned 0 times 11629920 (64.76%) aligned exactly 1 time 5603783 (31.21%) aligned >1 times 95.97% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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] 5205162 / 17233703 = 0.3020 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 03:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.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 03:21:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:21:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:21:50: 1000000 INFO @ Thu, 16 Apr 2020 03:21:55: 2000000 INFO @ Thu, 16 Apr 2020 03:22:01: 3000000 INFO @ Thu, 16 Apr 2020 03:22:06: 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 03:22:11: 5000000 INFO @ Thu, 16 Apr 2020 03:22:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.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 03:22:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:22:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:22:17: 6000000 INFO @ Thu, 16 Apr 2020 03:22:20: 1000000 INFO @ Thu, 16 Apr 2020 03:22:23: 7000000 INFO @ Thu, 16 Apr 2020 03:22:26: 2000000 INFO @ Thu, 16 Apr 2020 03:22:29: 8000000 INFO @ Thu, 16 Apr 2020 03:22:32: 3000000 INFO @ Thu, 16 Apr 2020 03:22:34: 9000000 INFO @ Thu, 16 Apr 2020 03:22:37: 4000000 INFO @ Thu, 16 Apr 2020 03:22:40: 10000000 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 03:22:43: 5000000 INFO @ Thu, 16 Apr 2020 03:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.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 03:22:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:22:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:22:46: 11000000 INFO @ Thu, 16 Apr 2020 03:22:49: 6000000 INFO @ Thu, 16 Apr 2020 03:22:50: 1000000 INFO @ Thu, 16 Apr 2020 03:22:52: 12000000 INFO @ Thu, 16 Apr 2020 03:22:52: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:22:52: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:22:52: #1 total tags in treatment: 12028541 INFO @ Thu, 16 Apr 2020 03:22:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:22:52: #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 03:22:52: #1 tags after filtering in treatment: 12028541 INFO @ Thu, 16 Apr 2020 03:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:22:52: #1 finished! INFO @ Thu, 16 Apr 2020 03:22:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:22:53: #2 number of paired peaks: 102 WARNING @ Thu, 16 Apr 2020 03:22:53: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Thu, 16 Apr 2020 03:22:53: start model_add_line... INFO @ Thu, 16 Apr 2020 03:22:53: start X-correlation... INFO @ Thu, 16 Apr 2020 03:22:53: end of X-cor INFO @ Thu, 16 Apr 2020 03:22:53: #2 finished! INFO @ Thu, 16 Apr 2020 03:22:53: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:22:53: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 03:22:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.05_model.r WARNING @ Thu, 16 Apr 2020 03:22:53: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:22:53: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 03:22:53: #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 03:22:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:22:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:22:55: 7000000 INFO @ Thu, 16 Apr 2020 03:22:56: 2000000 INFO @ Thu, 16 Apr 2020 03:23:01: 8000000 INFO @ Thu, 16 Apr 2020 03:23:01: 3000000 INFO @ Thu, 16 Apr 2020 03:23:07: 9000000 INFO @ Thu, 16 Apr 2020 03:23:07: 4000000 INFO @ Thu, 16 Apr 2020 03:23:12: 10000000 INFO @ Thu, 16 Apr 2020 03:23:13: 5000000 INFO @ Thu, 16 Apr 2020 03:23:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:23:18: 11000000 INFO @ Thu, 16 Apr 2020 03:23:19: 6000000 INFO @ Thu, 16 Apr 2020 03:23:24: 12000000 INFO @ Thu, 16 Apr 2020 03:23:24: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:23:24: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:23:24: #1 total tags in treatment: 12028541 INFO @ Thu, 16 Apr 2020 03:23:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:23:24: #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 03:23:24: #1 tags after filtering in treatment: 12028541 INFO @ Thu, 16 Apr 2020 03:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:23:24: #1 finished! INFO @ Thu, 16 Apr 2020 03:23:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:23:25: 7000000 INFO @ Thu, 16 Apr 2020 03:23:25: #2 number of paired peaks: 102 WARNING @ Thu, 16 Apr 2020 03:23:25: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Thu, 16 Apr 2020 03:23:25: start model_add_line... INFO @ Thu, 16 Apr 2020 03:23:25: start X-correlation... INFO @ Thu, 16 Apr 2020 03:23:25: end of X-cor INFO @ Thu, 16 Apr 2020 03:23:25: #2 finished! INFO @ Thu, 16 Apr 2020 03:23:25: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:23:25: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 03:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.10_model.r WARNING @ Thu, 16 Apr 2020 03:23:25: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:23:25: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 03:23:25: #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 03:23:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:23:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:23:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:23:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.05_summits.bed INFO @ Thu, 16 Apr 2020 03:23:28: Done! INFO @ Thu, 16 Apr 2020 03:23:30: 8000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2484 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:23:36: 9000000 INFO @ Thu, 16 Apr 2020 03:23:41: 10000000 INFO @ Thu, 16 Apr 2020 03:23:47: 11000000 INFO @ Thu, 16 Apr 2020 03:23:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:23:53: 12000000 INFO @ Thu, 16 Apr 2020 03:23:53: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:23:53: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:23:53: #1 total tags in treatment: 12028541 INFO @ Thu, 16 Apr 2020 03:23:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:23:53: #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 03:23:53: #1 tags after filtering in treatment: 12028541 INFO @ Thu, 16 Apr 2020 03:23:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:23:53: #1 finished! INFO @ Thu, 16 Apr 2020 03:23:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:23:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:23:54: #2 number of paired peaks: 102 WARNING @ Thu, 16 Apr 2020 03:23:54: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Thu, 16 Apr 2020 03:23:54: start model_add_line... INFO @ Thu, 16 Apr 2020 03:23:54: start X-correlation... INFO @ Thu, 16 Apr 2020 03:23:54: end of X-cor INFO @ Thu, 16 Apr 2020 03:23:54: #2 finished! INFO @ Thu, 16 Apr 2020 03:23:54: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:23:54: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 03:23:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.20_model.r WARNING @ Thu, 16 Apr 2020 03:23:54: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:23:54: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 03:23:54: #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 03:23:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:23:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:24:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:24:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:24:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.10_summits.bed INFO @ Thu, 16 Apr 2020 03:24:00: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1116 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:24:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:24:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:24:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:24:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775932/SRX5775932.20_summits.bed INFO @ Thu, 16 Apr 2020 03:24:28: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (434 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。