Job ID = 5720879 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:48:21 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 ) 2020-04-15T17:48:21 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 ) 2020-04-15T17:49:39 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 ) 2020-04-15T17:49:39 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 : 20,513,666 reads read : 20,513,666 reads written : 20,513,666 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: 00:04:38 20513666 reads; of these: 20513666 (100.00%) were unpaired; of these: 14927990 (72.77%) aligned 0 times 3808895 (18.57%) aligned exactly 1 time 1776781 (8.66%) aligned >1 times 27.23% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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_rmdupse_core] 1797943 / 5585676 = 0.3219 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 02:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.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 02:58:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:58:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:58:43: 1000000 INFO @ Thu, 16 Apr 2020 02:58:50: 2000000 INFO @ Thu, 16 Apr 2020 02:58:57: 3000000 INFO @ Thu, 16 Apr 2020 02:59:03: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 02:59:03: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 02:59:03: #1 total tags in treatment: 3787733 INFO @ Thu, 16 Apr 2020 02:59:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:59:03: #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 02:59:03: #1 tags after filtering in treatment: 3787733 INFO @ Thu, 16 Apr 2020 02:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:59:03: #1 finished! INFO @ Thu, 16 Apr 2020 02:59:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:59:03: #2 number of paired peaks: 828 WARNING @ Thu, 16 Apr 2020 02:59:03: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Thu, 16 Apr 2020 02:59:03: start model_add_line... INFO @ Thu, 16 Apr 2020 02:59:03: start X-correlation... INFO @ Thu, 16 Apr 2020 02:59:03: end of X-cor INFO @ Thu, 16 Apr 2020 02:59:03: #2 finished! INFO @ Thu, 16 Apr 2020 02:59:03: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 02:59:03: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 02:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.05_model.r WARNING @ Thu, 16 Apr 2020 02:59:03: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:59:03: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 02:59:03: #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 02:59:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:59:03: #3 Pre-compute pvalue-qvalue table... 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 02:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.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 02:59:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:59:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:59:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:59:12: 1000000 INFO @ Thu, 16 Apr 2020 02:59:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:59:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:59:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.05_summits.bed INFO @ Thu, 16 Apr 2020 02:59:16: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1986 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:59:18: 2000000 INFO @ Thu, 16 Apr 2020 02:59:24: 3000000 INFO @ Thu, 16 Apr 2020 02:59:29: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 02:59:29: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 02:59:29: #1 total tags in treatment: 3787733 INFO @ Thu, 16 Apr 2020 02:59:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:59:29: #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 02:59:29: #1 tags after filtering in treatment: 3787733 INFO @ Thu, 16 Apr 2020 02:59:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:59:29: #1 finished! INFO @ Thu, 16 Apr 2020 02:59:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:59:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:59:30: #2 number of paired peaks: 828 WARNING @ Thu, 16 Apr 2020 02:59:30: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Thu, 16 Apr 2020 02:59:30: start model_add_line... INFO @ Thu, 16 Apr 2020 02:59:30: start X-correlation... INFO @ Thu, 16 Apr 2020 02:59:30: end of X-cor INFO @ Thu, 16 Apr 2020 02:59:30: #2 finished! INFO @ Thu, 16 Apr 2020 02:59:30: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 02:59:30: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 02:59:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.10_model.r WARNING @ Thu, 16 Apr 2020 02:59:30: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:59:30: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 02:59:30: #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 02:59:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:59:30: #3 Pre-compute pvalue-qvalue table... 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 02:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.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 02:59:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:59:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:59:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:59:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:59:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:59:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.10_summits.bed INFO @ Thu, 16 Apr 2020 02:59:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1210 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:59:42: 1000000 INFO @ Thu, 16 Apr 2020 02:59:49: 2000000 INFO @ Thu, 16 Apr 2020 02:59:56: 3000000 INFO @ Thu, 16 Apr 2020 03:00:02: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:00:02: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:00:02: #1 total tags in treatment: 3787733 INFO @ Thu, 16 Apr 2020 03:00:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:00:02: #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 03:00:02: #1 tags after filtering in treatment: 3787733 INFO @ Thu, 16 Apr 2020 03:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:00:02: #1 finished! INFO @ Thu, 16 Apr 2020 03:00:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:00:02: #2 number of paired peaks: 828 WARNING @ Thu, 16 Apr 2020 03:00:02: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Thu, 16 Apr 2020 03:00:02: start model_add_line... INFO @ Thu, 16 Apr 2020 03:00:02: start X-correlation... INFO @ Thu, 16 Apr 2020 03:00:02: end of X-cor INFO @ Thu, 16 Apr 2020 03:00:02: #2 finished! INFO @ Thu, 16 Apr 2020 03:00:02: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:00:02: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 03:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.20_model.r WARNING @ Thu, 16 Apr 2020 03:00:02: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:00:02: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 03:00:02: #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 03:00:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:00:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:00:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:00:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:00:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775907/SRX5775907.20_summits.bed INFO @ Thu, 16 Apr 2020 03:00:14: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (767 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。