Job ID = 6627135 SRX = SRX8521293 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:12:35 prefetch.2.10.7: 1) Downloading 'SRR11978466'... 2020-07-14T01:12:35 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:14:10 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:14:11 prefetch.2.10.7: 'SRR11978466' is valid 2020-07-14T01:14:11 prefetch.2.10.7: 1) 'SRR11978466' was downloaded successfully 2020-07-14T01:14:11 prefetch.2.10.7: 'SRR11978466' has 0 unresolved dependencies Read 11051429 spots for SRR11978466/SRR11978466.sra Written 11051429 spots for SRR11978466/SRR11978466.sra 2020-07-14T01:15:09 prefetch.2.10.7: 1) Downloading 'SRR11978467'... 2020-07-14T01:15:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:16:59 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:17:00 prefetch.2.10.7: 'SRR11978467' is valid 2020-07-14T01:17:00 prefetch.2.10.7: 1) 'SRR11978467' was downloaded successfully 2020-07-14T01:17:00 prefetch.2.10.7: 'SRR11978467' has 0 unresolved dependencies Read 11026052 spots for SRR11978467/SRR11978467.sra Written 11026052 spots for SRR11978467/SRR11978467.sra 2020-07-14T01:17:51 prefetch.2.10.7: 1) Downloading 'SRR11978468'... 2020-07-14T01:17:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:19:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:19:12 prefetch.2.10.7: 'SRR11978468' is valid 2020-07-14T01:19:12 prefetch.2.10.7: 1) 'SRR11978468' was downloaded successfully 2020-07-14T01:19:12 prefetch.2.10.7: 'SRR11978468' has 0 unresolved dependencies Read 10953135 spots for SRR11978468/SRR11978468.sra Written 10953135 spots for SRR11978468/SRR11978468.sra 2020-07-14T01:20:00 prefetch.2.10.7: 1) Downloading 'SRR11978469'... 2020-07-14T01:20:00 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:21:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:21:32 prefetch.2.10.7: 'SRR11978469' is valid 2020-07-14T01:21:32 prefetch.2.10.7: 1) 'SRR11978469' was downloaded successfully 2020-07-14T01:21:32 prefetch.2.10.7: 'SRR11978469' has 0 unresolved dependencies Read 11140708 spots for SRR11978469/SRR11978469.sra Written 11140708 spots for SRR11978469/SRR11978469.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627392 ("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: 00:06:14 44171324 reads; of these: 44171324 (100.00%) were unpaired; of these: 38367275 (86.86%) aligned 0 times 4422800 (10.01%) aligned exactly 1 time 1381249 (3.13%) aligned >1 times 13.14% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 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] 1025048 / 5804049 = 0.1766 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 10:30:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.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 10:30:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:30:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:30:55: 1000000 INFO @ Tue, 14 Jul 2020 10:31:01: 2000000 INFO @ Tue, 14 Jul 2020 10:31:08: 3000000 INFO @ Tue, 14 Jul 2020 10:31:15: 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 @ Tue, 14 Jul 2020 10:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.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 10:31:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:31:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:31:21: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:31:21: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:31:21: #1 total tags in treatment: 4779001 INFO @ Tue, 14 Jul 2020 10:31:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:31:21: #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 10:31:21: #1 tags after filtering in treatment: 4779001 INFO @ Tue, 14 Jul 2020 10:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:31:21: #1 finished! INFO @ Tue, 14 Jul 2020 10:31:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:31:21: #2 number of paired peaks: 517 WARNING @ Tue, 14 Jul 2020 10:31:21: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 14 Jul 2020 10:31:21: start model_add_line... INFO @ Tue, 14 Jul 2020 10:31:21: start X-correlation... INFO @ Tue, 14 Jul 2020 10:31:21: end of X-cor INFO @ Tue, 14 Jul 2020 10:31:21: #2 finished! INFO @ Tue, 14 Jul 2020 10:31:21: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 10:31:21: #2 alternative fragment length(s) may be 66,527 bps INFO @ Tue, 14 Jul 2020 10:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.05_model.r WARNING @ Tue, 14 Jul 2020 10:31:21: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:31:21: #2 You may need to consider one of the other alternative d(s): 66,527 WARNING @ Tue, 14 Jul 2020 10:31:21: #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 10:31:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:31:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:31:24: 1000000 INFO @ Tue, 14 Jul 2020 10:31:30: 2000000 INFO @ Tue, 14 Jul 2020 10:31:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:31:36: 3000000 INFO @ Tue, 14 Jul 2020 10:31:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:31:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:31:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.05_summits.bed INFO @ Tue, 14 Jul 2020 10:31:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2039 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:31:42: 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 @ Tue, 14 Jul 2020 10:31:47: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:31:47: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:31:47: #1 total tags in treatment: 4779001 INFO @ Tue, 14 Jul 2020 10:31:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:31:47: #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 10:31:47: #1 tags after filtering in treatment: 4779001 INFO @ Tue, 14 Jul 2020 10:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:31:47: #1 finished! INFO @ Tue, 14 Jul 2020 10:31:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.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 10:31:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:31:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:31:48: #2 number of paired peaks: 517 WARNING @ Tue, 14 Jul 2020 10:31:48: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 14 Jul 2020 10:31:48: start model_add_line... INFO @ Tue, 14 Jul 2020 10:31:48: start X-correlation... INFO @ Tue, 14 Jul 2020 10:31:48: end of X-cor INFO @ Tue, 14 Jul 2020 10:31:48: #2 finished! INFO @ Tue, 14 Jul 2020 10:31:48: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 10:31:48: #2 alternative fragment length(s) may be 66,527 bps INFO @ Tue, 14 Jul 2020 10:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.10_model.r WARNING @ Tue, 14 Jul 2020 10:31:48: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:31:48: #2 You may need to consider one of the other alternative d(s): 66,527 WARNING @ Tue, 14 Jul 2020 10:31:48: #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 10:31:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:31:55: 1000000 INFO @ Tue, 14 Jul 2020 10:31:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:32:02: 2000000 INFO @ Tue, 14 Jul 2020 10:32:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:32:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:32:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.10_summits.bed INFO @ Tue, 14 Jul 2020 10:32:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (901 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:32:08: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:32:15: 4000000 INFO @ Tue, 14 Jul 2020 10:32:21: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 10:32:21: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 10:32:21: #1 total tags in treatment: 4779001 INFO @ Tue, 14 Jul 2020 10:32:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:32:21: #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 10:32:21: #1 tags after filtering in treatment: 4779001 INFO @ Tue, 14 Jul 2020 10:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:32:21: #1 finished! INFO @ Tue, 14 Jul 2020 10:32:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:32:21: #2 number of paired peaks: 517 WARNING @ Tue, 14 Jul 2020 10:32:21: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 14 Jul 2020 10:32:21: start model_add_line... INFO @ Tue, 14 Jul 2020 10:32:21: start X-correlation... INFO @ Tue, 14 Jul 2020 10:32:21: end of X-cor INFO @ Tue, 14 Jul 2020 10:32:21: #2 finished! INFO @ Tue, 14 Jul 2020 10:32:21: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 10:32:21: #2 alternative fragment length(s) may be 66,527 bps INFO @ Tue, 14 Jul 2020 10:32:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.20_model.r WARNING @ Tue, 14 Jul 2020 10:32:21: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:32:21: #2 You may need to consider one of the other alternative d(s): 66,527 WARNING @ Tue, 14 Jul 2020 10:32:21: #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 10:32:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:32:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:32:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:32:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:32:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:32:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521293/SRX8521293.20_summits.bed INFO @ Tue, 14 Jul 2020 10:32:36: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (250 records, 4 fields): 2 millis CompletedMACS2peakCalling