Job ID = 6627103 SRX = SRX8521286 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T00:54:22 prefetch.2.10.7: 1) Downloading 'SRR11978434'... 2020-07-14T00:54:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:56:39 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:56:40 prefetch.2.10.7: 'SRR11978434' is valid 2020-07-14T00:56:40 prefetch.2.10.7: 1) 'SRR11978434' was downloaded successfully 2020-07-14T00:56:40 prefetch.2.10.7: 'SRR11978434' has 0 unresolved dependencies Read 11455722 spots for SRR11978434/SRR11978434.sra Written 11455722 spots for SRR11978434/SRR11978434.sra 2020-07-14T00:57:28 prefetch.2.10.7: 1) Downloading 'SRR11978435'... 2020-07-14T00:57:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:59:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:59:04 prefetch.2.10.7: 'SRR11978435' is valid 2020-07-14T00:59:04 prefetch.2.10.7: 1) 'SRR11978435' was downloaded successfully 2020-07-14T00:59:04 prefetch.2.10.7: 'SRR11978435' has 0 unresolved dependencies Read 11415103 spots for SRR11978435/SRR11978435.sra Written 11415103 spots for SRR11978435/SRR11978435.sra 2020-07-14T00:59:52 prefetch.2.10.7: 1) Downloading 'SRR11978436'... 2020-07-14T00:59:52 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:01:18 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:01:18 prefetch.2.10.7: 'SRR11978436' is valid 2020-07-14T01:01:18 prefetch.2.10.7: 1) 'SRR11978436' was downloaded successfully 2020-07-14T01:01:18 prefetch.2.10.7: 'SRR11978436' has 0 unresolved dependencies Read 11753372 spots for SRR11978436/SRR11978436.sra Written 11753372 spots for SRR11978436/SRR11978436.sra 2020-07-14T01:02:11 prefetch.2.10.7: 1) Downloading 'SRR11978437'... 2020-07-14T01:02:11 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:05:33 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:05:33 prefetch.2.10.7: 'SRR11978437' is valid 2020-07-14T01:05:33 prefetch.2.10.7: 1) 'SRR11978437' was downloaded successfully 2020-07-14T01:05:33 prefetch.2.10.7: 'SRR11978437' has 0 unresolved dependencies Read 11732208 spots for SRR11978437/SRR11978437.sra Written 11732208 spots for SRR11978437/SRR11978437.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627342 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:26 46356405 reads; of these: 46356405 (100.00%) were unpaired; of these: 40509782 (87.39%) aligned 0 times 4502329 (9.71%) aligned exactly 1 time 1344294 (2.90%) aligned >1 times 12.61% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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_rmdupse_core] 1319672 / 5846623 = 0.2257 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 @ Tue, 14 Jul 2020 10:16:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.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 @ Tue, 14 Jul 2020 10:16:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:16:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:16:12: 1000000 INFO @ Tue, 14 Jul 2020 10:16:18: 2000000 INFO @ Tue, 14 Jul 2020 10:16:24: 3000000 INFO @ Tue, 14 Jul 2020 10:16:29: 4000000 INFO @ Tue, 14 Jul 2020 10:16:32: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:16:32: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:16:32: #1 total tags in treatment: 4526951 INFO @ Tue, 14 Jul 2020 10:16:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:16:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:16:32: #1 tags after filtering in treatment: 4526951 INFO @ Tue, 14 Jul 2020 10:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:16:32: #1 finished! INFO @ Tue, 14 Jul 2020 10:16:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:16:33: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 10:16:33: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 10:16:33: start model_add_line... INFO @ Tue, 14 Jul 2020 10:16:33: start X-correlation... INFO @ Tue, 14 Jul 2020 10:16:33: end of X-cor INFO @ Tue, 14 Jul 2020 10:16:33: #2 finished! INFO @ Tue, 14 Jul 2020 10:16:33: #2 predicted fragment length is 70 bps INFO @ Tue, 14 Jul 2020 10:16:33: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 14 Jul 2020 10:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.05_model.r WARNING @ Tue, 14 Jul 2020 10:16:33: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:16:33: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 14 Jul 2020 10:16:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:16:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:16:33: #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 @ Tue, 14 Jul 2020 10:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.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 @ Tue, 14 Jul 2020 10:16:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:16:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:16:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:16:42: 1000000 INFO @ Tue, 14 Jul 2020 10:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.05_summits.bed INFO @ Tue, 14 Jul 2020 10:16:47: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1771 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:16:48: 2000000 INFO @ Tue, 14 Jul 2020 10:16:54: 3000000 INFO @ Tue, 14 Jul 2020 10:17:00: 4000000 INFO @ Tue, 14 Jul 2020 10:17:03: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:17:03: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:17:03: #1 total tags in treatment: 4526951 INFO @ Tue, 14 Jul 2020 10:17:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:17:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:17:03: #1 tags after filtering in treatment: 4526951 INFO @ Tue, 14 Jul 2020 10:17:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:17:03: #1 finished! INFO @ Tue, 14 Jul 2020 10:17:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:17:03: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 10:17:03: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 10:17:03: start model_add_line... INFO @ Tue, 14 Jul 2020 10:17:04: start X-correlation... INFO @ Tue, 14 Jul 2020 10:17:04: end of X-cor INFO @ Tue, 14 Jul 2020 10:17:04: #2 finished! INFO @ Tue, 14 Jul 2020 10:17:04: #2 predicted fragment length is 70 bps INFO @ Tue, 14 Jul 2020 10:17:04: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 14 Jul 2020 10:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.10_model.r WARNING @ Tue, 14 Jul 2020 10:17:04: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:17:04: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 14 Jul 2020 10:17:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:17:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:17:04: #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 @ Tue, 14 Jul 2020 10:17:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.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 @ Tue, 14 Jul 2020 10:17:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:17:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:17:12: 1000000 INFO @ Tue, 14 Jul 2020 10:17:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:17:18: 2000000 INFO @ Tue, 14 Jul 2020 10:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.10_summits.bed INFO @ Tue, 14 Jul 2020 10:17:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:17:23: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:17:29: 4000000 INFO @ Tue, 14 Jul 2020 10:17:32: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:17:32: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:17:32: #1 total tags in treatment: 4526951 INFO @ Tue, 14 Jul 2020 10:17:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:17:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:17:32: #1 tags after filtering in treatment: 4526951 INFO @ Tue, 14 Jul 2020 10:17:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:17:32: #1 finished! INFO @ Tue, 14 Jul 2020 10:17:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:17:32: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 10:17:32: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 10:17:32: start model_add_line... INFO @ Tue, 14 Jul 2020 10:17:33: start X-correlation... INFO @ Tue, 14 Jul 2020 10:17:33: end of X-cor INFO @ Tue, 14 Jul 2020 10:17:33: #2 finished! INFO @ Tue, 14 Jul 2020 10:17:33: #2 predicted fragment length is 70 bps INFO @ Tue, 14 Jul 2020 10:17:33: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 14 Jul 2020 10:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.20_model.r WARNING @ Tue, 14 Jul 2020 10:17:33: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:17:33: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 14 Jul 2020 10:17:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:17:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:17:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:17:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:17:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:17:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:17:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521286/SRX8521286.20_summits.bed INFO @ Tue, 14 Jul 2020 10:17:47: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 2 millis CompletedMACS2peakCalling