Job ID = 5720768 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:23:32 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 ) 2020-04-15T16:23:32 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 : 11,457,696 reads read : 22,915,392 reads written : 11,457,696 reads 0-length : 11,457,696 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: 00:04:26 11457696 reads; of these: 11457696 (100.00%) were unpaired; of these: 762056 (6.65%) aligned 0 times 8186892 (71.45%) aligned exactly 1 time 2508748 (21.90%) aligned >1 times 93.35% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 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] 562175 / 10695640 = 0.0526 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 01:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.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 01:32:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:32:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:32:18: 1000000 INFO @ Thu, 16 Apr 2020 01:32:25: 2000000 INFO @ Thu, 16 Apr 2020 01:32:31: 3000000 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 01:32:38: 4000000 INFO @ Thu, 16 Apr 2020 01:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.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 01:32:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:32:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:32:45: 5000000 INFO @ Thu, 16 Apr 2020 01:32:47: 1000000 INFO @ Thu, 16 Apr 2020 01:32:52: 6000000 INFO @ Thu, 16 Apr 2020 01:32:54: 2000000 INFO @ Thu, 16 Apr 2020 01:33:00: 7000000 INFO @ Thu, 16 Apr 2020 01:33:02: 3000000 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 01:33:07: 8000000 INFO @ Thu, 16 Apr 2020 01:33:09: 4000000 INFO @ Thu, 16 Apr 2020 01:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.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 01:33:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:33:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:33:14: 9000000 INFO @ Thu, 16 Apr 2020 01:33:16: 1000000 INFO @ Thu, 16 Apr 2020 01:33:16: 5000000 INFO @ Thu, 16 Apr 2020 01:33:21: 10000000 INFO @ Thu, 16 Apr 2020 01:33:22: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:33:22: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:33:22: #1 total tags in treatment: 10133465 INFO @ Thu, 16 Apr 2020 01:33:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:33:22: #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 01:33:22: #1 tags after filtering in treatment: 10133465 INFO @ Thu, 16 Apr 2020 01:33:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:33:22: #1 finished! INFO @ Thu, 16 Apr 2020 01:33:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:33:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:33:23: 2000000 INFO @ Thu, 16 Apr 2020 01:33:23: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 01:33:23: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 01:33:23: start model_add_line... INFO @ Thu, 16 Apr 2020 01:33:23: start X-correlation... INFO @ Thu, 16 Apr 2020 01:33:23: end of X-cor INFO @ Thu, 16 Apr 2020 01:33:23: #2 finished! INFO @ Thu, 16 Apr 2020 01:33:23: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:33:23: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.05_model.r WARNING @ Thu, 16 Apr 2020 01:33:23: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:33:23: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:33:23: #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 01:33:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:33:23: 6000000 INFO @ Thu, 16 Apr 2020 01:33:29: 3000000 INFO @ Thu, 16 Apr 2020 01:33:31: 7000000 INFO @ Thu, 16 Apr 2020 01:33:36: 4000000 INFO @ Thu, 16 Apr 2020 01:33:38: 8000000 INFO @ Thu, 16 Apr 2020 01:33:42: 5000000 INFO @ Thu, 16 Apr 2020 01:33:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:33:45: 9000000 INFO @ Thu, 16 Apr 2020 01:33:49: 6000000 INFO @ Thu, 16 Apr 2020 01:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:33:52: 10000000 INFO @ Thu, 16 Apr 2020 01:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.05_summits.bed INFO @ Thu, 16 Apr 2020 01:33:52: Done! INFO @ Thu, 16 Apr 2020 01:33:53: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:33:53: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:33:53: #1 total tags in treatment: 10133465 INFO @ Thu, 16 Apr 2020 01:33:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:33:53: #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 01:33:53: #1 tags after filtering in treatment: 10133465 INFO @ Thu, 16 Apr 2020 01:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:33:53: #1 finished! INFO @ Thu, 16 Apr 2020 01:33:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:33:54: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 01:33:54: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 01:33:54: start model_add_line... INFO @ Thu, 16 Apr 2020 01:33:54: start X-correlation... INFO @ Thu, 16 Apr 2020 01:33:54: end of X-cor INFO @ Thu, 16 Apr 2020 01:33:54: #2 finished! INFO @ Thu, 16 Apr 2020 01:33:54: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:33:54: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.10_model.r WARNING @ Thu, 16 Apr 2020 01:33:54: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:33:54: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:33:54: #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 01:33:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:33:55: 7000000 pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1010 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:34:01: 8000000 INFO @ Thu, 16 Apr 2020 01:34:07: 9000000 INFO @ Thu, 16 Apr 2020 01:34:12: 10000000 INFO @ Thu, 16 Apr 2020 01:34:13: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:34:13: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:34:13: #1 total tags in treatment: 10133465 INFO @ Thu, 16 Apr 2020 01:34:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:34:13: #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 01:34:13: #1 tags after filtering in treatment: 10133465 INFO @ Thu, 16 Apr 2020 01:34:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:34:13: #1 finished! INFO @ Thu, 16 Apr 2020 01:34:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:34:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:34:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:34:14: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 01:34:14: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 01:34:14: start model_add_line... INFO @ Thu, 16 Apr 2020 01:34:14: start X-correlation... INFO @ Thu, 16 Apr 2020 01:34:14: end of X-cor INFO @ Thu, 16 Apr 2020 01:34:14: #2 finished! INFO @ Thu, 16 Apr 2020 01:34:14: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:34:14: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:34:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.20_model.r WARNING @ Thu, 16 Apr 2020 01:34:14: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:34:14: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:34:14: #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 01:34:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:34:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.10_summits.bed INFO @ Thu, 16 Apr 2020 01:34:24: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (539 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:34:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227005/SRX5227005.20_summits.bed INFO @ Thu, 16 Apr 2020 01:34:43: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (282 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。