Job ID = 5720898 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:53:19 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 ) 2020-04-15T17:53:19 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 ) 2020-04-15T17:55:50 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 ) 2020-04-15T17:55:50 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 : 17,109,992 reads read : 17,109,992 reads written : 17,109,992 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: 00:07:13 17109992 reads; of these: 17109992 (100.00%) were unpaired; of these: 635045 (3.71%) aligned 0 times 11152139 (65.18%) aligned exactly 1 time 5322808 (31.11%) aligned >1 times 96.29% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 4840506 / 16474947 = 0.2938 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 03:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.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 03:11:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:11:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:11:38: 1000000 INFO @ Thu, 16 Apr 2020 03:11:44: 2000000 INFO @ Thu, 16 Apr 2020 03:11:50: 3000000 INFO @ Thu, 16 Apr 2020 03:11:56: 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 03:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.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 03:12:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:12:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:12:02: 5000000 INFO @ Thu, 16 Apr 2020 03:12:08: 1000000 INFO @ Thu, 16 Apr 2020 03:12:09: 6000000 INFO @ Thu, 16 Apr 2020 03:12:15: 2000000 INFO @ Thu, 16 Apr 2020 03:12:16: 7000000 INFO @ Thu, 16 Apr 2020 03:12:22: 3000000 INFO @ Thu, 16 Apr 2020 03:12:23: 8000000 INFO @ Thu, 16 Apr 2020 03:12:29: 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 03:12:30: 9000000 INFO @ Thu, 16 Apr 2020 03:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.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 03:12:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:12:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:12:36: 5000000 INFO @ Thu, 16 Apr 2020 03:12:37: 10000000 INFO @ Thu, 16 Apr 2020 03:12:38: 1000000 INFO @ Thu, 16 Apr 2020 03:12:43: 6000000 INFO @ Thu, 16 Apr 2020 03:12:44: 11000000 INFO @ Thu, 16 Apr 2020 03:12:45: 2000000 INFO @ Thu, 16 Apr 2020 03:12:48: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:12:48: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:12:48: #1 total tags in treatment: 11634441 INFO @ Thu, 16 Apr 2020 03:12:48: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:12:48: #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 03:12:48: #1 tags after filtering in treatment: 11634441 INFO @ Thu, 16 Apr 2020 03:12:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:12:48: #1 finished! INFO @ Thu, 16 Apr 2020 03:12:48: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:12:49: #2 number of paired peaks: 113 WARNING @ Thu, 16 Apr 2020 03:12:49: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Thu, 16 Apr 2020 03:12:49: start model_add_line... INFO @ Thu, 16 Apr 2020 03:12:49: start X-correlation... INFO @ Thu, 16 Apr 2020 03:12:49: end of X-cor INFO @ Thu, 16 Apr 2020 03:12:49: #2 finished! INFO @ Thu, 16 Apr 2020 03:12:49: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:12:49: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 16 Apr 2020 03:12:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.05_model.r WARNING @ Thu, 16 Apr 2020 03:12:49: #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 03:12:49: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 16 Apr 2020 03:12:49: #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 03:12:49: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:12:50: 7000000 INFO @ Thu, 16 Apr 2020 03:12:52: 3000000 INFO @ Thu, 16 Apr 2020 03:12:56: 8000000 INFO @ Thu, 16 Apr 2020 03:12:59: 4000000 INFO @ Thu, 16 Apr 2020 03:13:03: 9000000 INFO @ Thu, 16 Apr 2020 03:13:06: 5000000 INFO @ Thu, 16 Apr 2020 03:13:10: 10000000 INFO @ Thu, 16 Apr 2020 03:13:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:13:13: 6000000 INFO @ Thu, 16 Apr 2020 03:13:17: 11000000 INFO @ Thu, 16 Apr 2020 03:13:20: 7000000 INFO @ Thu, 16 Apr 2020 03:13:22: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:13:22: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:13:22: #1 total tags in treatment: 11634441 INFO @ Thu, 16 Apr 2020 03:13:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:13:22: #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 03:13:22: #1 tags after filtering in treatment: 11634441 INFO @ Thu, 16 Apr 2020 03:13:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:13:22: #1 finished! INFO @ Thu, 16 Apr 2020 03:13:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:13:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:13:22: #2 number of paired peaks: 113 WARNING @ Thu, 16 Apr 2020 03:13:22: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Thu, 16 Apr 2020 03:13:22: start model_add_line... INFO @ Thu, 16 Apr 2020 03:13:23: start X-correlation... INFO @ Thu, 16 Apr 2020 03:13:23: end of X-cor INFO @ Thu, 16 Apr 2020 03:13:23: #2 finished! INFO @ Thu, 16 Apr 2020 03:13:23: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:13:23: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 16 Apr 2020 03:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.10_model.r WARNING @ Thu, 16 Apr 2020 03:13:23: #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 03:13:23: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 16 Apr 2020 03:13:23: #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 03:13:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.05_summits.bed INFO @ Thu, 16 Apr 2020 03:13:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2404 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:13:26: 8000000 INFO @ Thu, 16 Apr 2020 03:13:33: 9000000 INFO @ Thu, 16 Apr 2020 03:13:39: 10000000 INFO @ Thu, 16 Apr 2020 03:13:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:13:46: 11000000 INFO @ Thu, 16 Apr 2020 03:13:50: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:13:50: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:13:50: #1 total tags in treatment: 11634441 INFO @ Thu, 16 Apr 2020 03:13:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:13:50: #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 03:13:50: #1 tags after filtering in treatment: 11634441 INFO @ Thu, 16 Apr 2020 03:13:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:13:50: #1 finished! INFO @ Thu, 16 Apr 2020 03:13:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:13:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:13:51: #2 number of paired peaks: 113 WARNING @ Thu, 16 Apr 2020 03:13:51: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Thu, 16 Apr 2020 03:13:51: start model_add_line... INFO @ Thu, 16 Apr 2020 03:13:51: start X-correlation... INFO @ Thu, 16 Apr 2020 03:13:51: end of X-cor INFO @ Thu, 16 Apr 2020 03:13:51: #2 finished! INFO @ Thu, 16 Apr 2020 03:13:51: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 03:13:51: #2 alternative fragment length(s) may be 4,75 bps INFO @ Thu, 16 Apr 2020 03:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.20_model.r WARNING @ Thu, 16 Apr 2020 03:13:51: #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 03:13:51: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Thu, 16 Apr 2020 03:13:51: #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 03:13:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:13:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.10_summits.bed INFO @ Thu, 16 Apr 2020 03:13:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (928 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:14:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775926/SRX5775926.20_summits.bed INFO @ Thu, 16 Apr 2020 03:14:25: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (408 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。