Job ID = 5720887 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:01:02 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 ) 2020-04-15T18:01:02 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 ) 2020-04-15T18:01:02 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 : 24,024,039 reads read : 24,024,039 reads written : 24,024,039 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: 00:10:17 24024039 reads; of these: 24024039 (100.00%) were unpaired; of these: 1459364 (6.07%) aligned 0 times 15372417 (63.99%) aligned exactly 1 time 7192258 (29.94%) aligned >1 times 93.93% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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] 14046199 / 22564675 = 0.6225 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 03:17:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.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 03:17:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:17:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:17:23: 1000000 INFO @ Thu, 16 Apr 2020 03:17:28: 2000000 INFO @ Thu, 16 Apr 2020 03:17:33: 3000000 INFO @ Thu, 16 Apr 2020 03:17:38: 4000000 INFO @ Thu, 16 Apr 2020 03:17:43: 5000000 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 03:17:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.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 03:17:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:17:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:17:48: 6000000 INFO @ Thu, 16 Apr 2020 03:17:53: 1000000 INFO @ Thu, 16 Apr 2020 03:17:53: 7000000 INFO @ Thu, 16 Apr 2020 03:17:58: 2000000 INFO @ Thu, 16 Apr 2020 03:17:59: 8000000 INFO @ Thu, 16 Apr 2020 03:18:01: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:18:01: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:18:01: #1 total tags in treatment: 8518476 INFO @ Thu, 16 Apr 2020 03:18:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:18:01: #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 03:18:01: #1 tags after filtering in treatment: 8518476 INFO @ Thu, 16 Apr 2020 03:18:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:18:01: #1 finished! INFO @ Thu, 16 Apr 2020 03:18:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:18:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:18:02: #2 number of paired peaks: 536 WARNING @ Thu, 16 Apr 2020 03:18:02: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 16 Apr 2020 03:18:02: start model_add_line... INFO @ Thu, 16 Apr 2020 03:18:02: start X-correlation... INFO @ Thu, 16 Apr 2020 03:18:02: end of X-cor INFO @ Thu, 16 Apr 2020 03:18:02: #2 finished! INFO @ Thu, 16 Apr 2020 03:18:02: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 03:18:02: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 16 Apr 2020 03:18:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.05_model.r WARNING @ Thu, 16 Apr 2020 03:18:02: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:18:02: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 16 Apr 2020 03:18:02: #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 03:18:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:18:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:18:04: 3000000 INFO @ Thu, 16 Apr 2020 03:18:09: 4000000 INFO @ Thu, 16 Apr 2020 03:18:14: 5000000 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 03:18:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.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 03:18:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:18:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:18:19: 6000000 INFO @ Thu, 16 Apr 2020 03:18:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:18:24: 7000000 INFO @ Thu, 16 Apr 2020 03:18:24: 1000000 INFO @ Thu, 16 Apr 2020 03:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.05_summits.bed INFO @ Thu, 16 Apr 2020 03:18:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5023 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:18:29: 8000000 INFO @ Thu, 16 Apr 2020 03:18:30: 2000000 INFO @ Thu, 16 Apr 2020 03:18:32: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:18:32: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:18:32: #1 total tags in treatment: 8518476 INFO @ Thu, 16 Apr 2020 03:18:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:18:32: #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 03:18:32: #1 tags after filtering in treatment: 8518476 INFO @ Thu, 16 Apr 2020 03:18:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:18:32: #1 finished! INFO @ Thu, 16 Apr 2020 03:18:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:18:32: #2 number of paired peaks: 536 WARNING @ Thu, 16 Apr 2020 03:18:32: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 16 Apr 2020 03:18:32: start model_add_line... INFO @ Thu, 16 Apr 2020 03:18:33: start X-correlation... INFO @ Thu, 16 Apr 2020 03:18:33: end of X-cor INFO @ Thu, 16 Apr 2020 03:18:33: #2 finished! INFO @ Thu, 16 Apr 2020 03:18:33: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 03:18:33: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 16 Apr 2020 03:18:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.10_model.r WARNING @ Thu, 16 Apr 2020 03:18:33: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:18:33: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 16 Apr 2020 03:18:33: #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 03:18:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:18:36: 3000000 INFO @ Thu, 16 Apr 2020 03:18:42: 4000000 INFO @ Thu, 16 Apr 2020 03:18:49: 5000000 INFO @ Thu, 16 Apr 2020 03:18:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:18:55: 6000000 INFO @ Thu, 16 Apr 2020 03:18:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:18:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:18:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.10_summits.bed INFO @ Thu, 16 Apr 2020 03:18:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1847 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:19:01: 7000000 INFO @ Thu, 16 Apr 2020 03:19:07: 8000000 INFO @ Thu, 16 Apr 2020 03:19:10: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:19:10: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:19:10: #1 total tags in treatment: 8518476 INFO @ Thu, 16 Apr 2020 03:19:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:19:10: #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 03:19:10: #1 tags after filtering in treatment: 8518476 INFO @ Thu, 16 Apr 2020 03:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:19:10: #1 finished! INFO @ Thu, 16 Apr 2020 03:19:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:19:11: #2 number of paired peaks: 536 WARNING @ Thu, 16 Apr 2020 03:19:11: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Thu, 16 Apr 2020 03:19:11: start model_add_line... INFO @ Thu, 16 Apr 2020 03:19:11: start X-correlation... INFO @ Thu, 16 Apr 2020 03:19:11: end of X-cor INFO @ Thu, 16 Apr 2020 03:19:11: #2 finished! INFO @ Thu, 16 Apr 2020 03:19:11: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 03:19:11: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 16 Apr 2020 03:19:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.20_model.r WARNING @ Thu, 16 Apr 2020 03:19:11: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:19:11: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 16 Apr 2020 03:19:11: #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 03:19:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:19:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:19:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775915/SRX5775915.20_summits.bed INFO @ Thu, 16 Apr 2020 03:19:37: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (489 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。