Job ID = 5720741 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:16:06 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 ) 2020-04-15T16:16:06 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 : 22,124,699 reads read : 44,249,398 reads written : 22,124,699 reads 0-length : 22,124,699 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: 00:08:49 22124699 reads; of these: 22124699 (100.00%) were unpaired; of these: 772468 (3.49%) aligned 0 times 15840023 (71.59%) aligned exactly 1 time 5512208 (24.91%) aligned >1 times 96.51% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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] 2425024 / 21352231 = 0.1136 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 01:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.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 01:32:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:32:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:32:27: 1000000 INFO @ Thu, 16 Apr 2020 01:32:33: 2000000 INFO @ Thu, 16 Apr 2020 01:32:38: 3000000 INFO @ Thu, 16 Apr 2020 01:32:44: 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 01:32:50: 5000000 INFO @ Thu, 16 Apr 2020 01:32:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.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 01:32:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:32:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:32:56: 6000000 INFO @ Thu, 16 Apr 2020 01:32:58: 1000000 INFO @ Thu, 16 Apr 2020 01:33:01: 7000000 INFO @ Thu, 16 Apr 2020 01:33:04: 2000000 INFO @ Thu, 16 Apr 2020 01:33:07: 8000000 INFO @ Thu, 16 Apr 2020 01:33:11: 3000000 INFO @ Thu, 16 Apr 2020 01:33:13: 9000000 INFO @ Thu, 16 Apr 2020 01:33:17: 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 01:33:19: 10000000 INFO @ Thu, 16 Apr 2020 01:33:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.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 01:33:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:33:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:33:24: 5000000 INFO @ Thu, 16 Apr 2020 01:33:25: 11000000 INFO @ Thu, 16 Apr 2020 01:33:28: 1000000 INFO @ Thu, 16 Apr 2020 01:33:31: 6000000 INFO @ Thu, 16 Apr 2020 01:33:31: 12000000 INFO @ Thu, 16 Apr 2020 01:33:34: 2000000 INFO @ Thu, 16 Apr 2020 01:33:37: 13000000 INFO @ Thu, 16 Apr 2020 01:33:38: 7000000 INFO @ Thu, 16 Apr 2020 01:33:41: 3000000 INFO @ Thu, 16 Apr 2020 01:33:44: 14000000 INFO @ Thu, 16 Apr 2020 01:33:44: 8000000 INFO @ Thu, 16 Apr 2020 01:33:48: 4000000 INFO @ Thu, 16 Apr 2020 01:33:50: 15000000 INFO @ Thu, 16 Apr 2020 01:33:51: 9000000 INFO @ Thu, 16 Apr 2020 01:33:55: 5000000 INFO @ Thu, 16 Apr 2020 01:33:56: 16000000 INFO @ Thu, 16 Apr 2020 01:33:58: 10000000 INFO @ Thu, 16 Apr 2020 01:34:01: 6000000 INFO @ Thu, 16 Apr 2020 01:34:03: 17000000 INFO @ Thu, 16 Apr 2020 01:34:05: 11000000 INFO @ Thu, 16 Apr 2020 01:34:08: 7000000 INFO @ Thu, 16 Apr 2020 01:34:09: 18000000 INFO @ Thu, 16 Apr 2020 01:34:12: 12000000 INFO @ Thu, 16 Apr 2020 01:34:14: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:34:14: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:34:14: #1 total tags in treatment: 18927207 INFO @ Thu, 16 Apr 2020 01:34:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:34:14: #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 01:34:15: #1 tags after filtering in treatment: 18927207 INFO @ Thu, 16 Apr 2020 01:34:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:34:15: #1 finished! INFO @ Thu, 16 Apr 2020 01:34:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:34:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:34:15: 8000000 INFO @ Thu, 16 Apr 2020 01:34:16: #2 number of paired peaks: 507 WARNING @ Thu, 16 Apr 2020 01:34:16: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Thu, 16 Apr 2020 01:34:16: start model_add_line... INFO @ Thu, 16 Apr 2020 01:34:16: start X-correlation... INFO @ Thu, 16 Apr 2020 01:34:16: end of X-cor INFO @ Thu, 16 Apr 2020 01:34:16: #2 finished! INFO @ Thu, 16 Apr 2020 01:34:16: #2 predicted fragment length is 71 bps INFO @ Thu, 16 Apr 2020 01:34:16: #2 alternative fragment length(s) may be 4,71 bps INFO @ Thu, 16 Apr 2020 01:34:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.05_model.r WARNING @ Thu, 16 Apr 2020 01:34:16: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:34:16: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Thu, 16 Apr 2020 01:34:16: #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 01:34:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:34:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:34:18: 13000000 INFO @ Thu, 16 Apr 2020 01:34:22: 9000000 INFO @ Thu, 16 Apr 2020 01:34:25: 14000000 INFO @ Thu, 16 Apr 2020 01:34:28: 10000000 INFO @ Thu, 16 Apr 2020 01:34:32: 15000000 INFO @ Thu, 16 Apr 2020 01:34:34: 11000000 INFO @ Thu, 16 Apr 2020 01:34:38: 16000000 INFO @ Thu, 16 Apr 2020 01:34:41: 12000000 INFO @ Thu, 16 Apr 2020 01:34:45: 17000000 INFO @ Thu, 16 Apr 2020 01:34:48: 13000000 INFO @ Thu, 16 Apr 2020 01:34:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:34:51: 18000000 INFO @ Thu, 16 Apr 2020 01:34:54: 14000000 INFO @ Thu, 16 Apr 2020 01:34:58: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:34:58: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:34:58: #1 total tags in treatment: 18927207 INFO @ Thu, 16 Apr 2020 01:34:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:34:58: #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 01:34:58: #1 tags after filtering in treatment: 18927207 INFO @ Thu, 16 Apr 2020 01:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:34:58: #1 finished! INFO @ Thu, 16 Apr 2020 01:34:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:34:59: #2 number of paired peaks: 507 WARNING @ Thu, 16 Apr 2020 01:34:59: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Thu, 16 Apr 2020 01:34:59: start model_add_line... INFO @ Thu, 16 Apr 2020 01:34:59: start X-correlation... INFO @ Thu, 16 Apr 2020 01:34:59: end of X-cor INFO @ Thu, 16 Apr 2020 01:34:59: #2 finished! INFO @ Thu, 16 Apr 2020 01:34:59: #2 predicted fragment length is 71 bps INFO @ Thu, 16 Apr 2020 01:34:59: #2 alternative fragment length(s) may be 4,71 bps INFO @ Thu, 16 Apr 2020 01:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.10_model.r WARNING @ Thu, 16 Apr 2020 01:34:59: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:34:59: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Thu, 16 Apr 2020 01:34:59: #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 01:34:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:35:01: 15000000 INFO @ Thu, 16 Apr 2020 01:35:07: 16000000 INFO @ Thu, 16 Apr 2020 01:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.05_summits.bed INFO @ Thu, 16 Apr 2020 01:35:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5810 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:35:14: 17000000 INFO @ Thu, 16 Apr 2020 01:35:20: 18000000 INFO @ Thu, 16 Apr 2020 01:35:26: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:35:26: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:35:26: #1 total tags in treatment: 18927207 INFO @ Thu, 16 Apr 2020 01:35:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:35:26: #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 01:35:26: #1 tags after filtering in treatment: 18927207 INFO @ Thu, 16 Apr 2020 01:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:35:26: #1 finished! INFO @ Thu, 16 Apr 2020 01:35:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:35:28: #2 number of paired peaks: 507 WARNING @ Thu, 16 Apr 2020 01:35:28: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Thu, 16 Apr 2020 01:35:28: start model_add_line... INFO @ Thu, 16 Apr 2020 01:35:28: start X-correlation... INFO @ Thu, 16 Apr 2020 01:35:28: end of X-cor INFO @ Thu, 16 Apr 2020 01:35:28: #2 finished! INFO @ Thu, 16 Apr 2020 01:35:28: #2 predicted fragment length is 71 bps INFO @ Thu, 16 Apr 2020 01:35:28: #2 alternative fragment length(s) may be 4,71 bps INFO @ Thu, 16 Apr 2020 01:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.20_model.r WARNING @ Thu, 16 Apr 2020 01:35:28: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:35:28: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Thu, 16 Apr 2020 01:35:28: #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 01:35:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:35:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:35:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:35:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.10_summits.bed INFO @ Thu, 16 Apr 2020 01:35:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2685 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:36:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226980/SRX5226980.20_summits.bed INFO @ Thu, 16 Apr 2020 01:36:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1018 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。