Job ID = 16439312 SRX = SRX15206490 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:52:05 prefetch.2.10.7: 1) Downloading 'SRR19139309'... 2022-08-02T05:52:05 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:52:27 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:52:28 prefetch.2.10.7: 'SRR19139309' is valid 2022-08-02T05:52:28 prefetch.2.10.7: 1) 'SRR19139309' was downloaded successfully 2022-08-02T05:52:28 prefetch.2.10.7: 'SRR19139309' has 0 unresolved dependencies Read 10036601 spots for SRR19139309/SRR19139309.sra Written 10036601 spots for SRR19139309/SRR19139309.sra 2022-08-02T05:53:22 prefetch.2.10.7: 1) Downloading 'SRR19139310'... 2022-08-02T05:53:22 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:53:32 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:53:32 prefetch.2.10.7: 'SRR19139310' is valid 2022-08-02T05:53:32 prefetch.2.10.7: 1) 'SRR19139310' was downloaded successfully 2022-08-02T05:53:32 prefetch.2.10.7: 'SRR19139310' has 0 unresolved dependencies Read 3693113 spots for SRR19139310/SRR19139310.sra Written 3693113 spots for SRR19139310/SRR19139310.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439413 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:45 13729714 reads; of these: 13729714 (100.00%) were unpaired; of these: 7643557 (55.67%) aligned 0 times 3914788 (28.51%) aligned exactly 1 time 2171369 (15.82%) aligned >1 times 44.33% overall alignment rate Time searching: 00:09:46 Overall time: 00:09:46 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] 4111576 / 6086157 = 0.6756 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:06:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.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, 02 Aug 2022 15:06:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:06:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:06:20: 1000000 INFO @ Tue, 02 Aug 2022 15:06:32: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:06:32: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:06:32: #1 total tags in treatment: 1974581 INFO @ Tue, 02 Aug 2022 15:06:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:06:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:06:32: #1 tags after filtering in treatment: 1974581 INFO @ Tue, 02 Aug 2022 15:06:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:06:32: #1 finished! INFO @ Tue, 02 Aug 2022 15:06:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:06:32: #2 number of paired peaks: 825 WARNING @ Tue, 02 Aug 2022 15:06:32: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Tue, 02 Aug 2022 15:06:32: start model_add_line... INFO @ Tue, 02 Aug 2022 15:06:32: start X-correlation... INFO @ Tue, 02 Aug 2022 15:06:32: end of X-cor INFO @ Tue, 02 Aug 2022 15:06:32: #2 finished! INFO @ Tue, 02 Aug 2022 15:06:32: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 15:06:32: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 15:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.05_model.r WARNING @ Tue, 02 Aug 2022 15:06:32: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:06:32: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 15:06:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:06:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:06:32: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.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, 02 Aug 2022 15:06:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:06:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:06:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:06:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:06:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:06:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.05_summits.bed INFO @ Tue, 02 Aug 2022 15:06:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1050 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:06:50: 1000000 INFO @ Tue, 02 Aug 2022 15:07:02: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:07:02: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:07:02: #1 total tags in treatment: 1974581 INFO @ Tue, 02 Aug 2022 15:07:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:07:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:07:02: #1 tags after filtering in treatment: 1974581 INFO @ Tue, 02 Aug 2022 15:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:07:02: #1 finished! INFO @ Tue, 02 Aug 2022 15:07:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:07:02: #2 number of paired peaks: 825 WARNING @ Tue, 02 Aug 2022 15:07:02: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Tue, 02 Aug 2022 15:07:02: start model_add_line... INFO @ Tue, 02 Aug 2022 15:07:02: start X-correlation... INFO @ Tue, 02 Aug 2022 15:07:02: end of X-cor INFO @ Tue, 02 Aug 2022 15:07:02: #2 finished! INFO @ Tue, 02 Aug 2022 15:07:02: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 15:07:02: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 15:07:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.10_model.r WARNING @ Tue, 02 Aug 2022 15:07:02: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:07:02: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 15:07:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:07:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:07:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.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, 02 Aug 2022 15:07:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:07:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:07:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.10_summits.bed INFO @ Tue, 02 Aug 2022 15:07:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:07:18: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:07:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:07:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:07:28: #1 total tags in treatment: 1974581 INFO @ Tue, 02 Aug 2022 15:07:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:07:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:07:28: #1 tags after filtering in treatment: 1974581 INFO @ Tue, 02 Aug 2022 15:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:07:28: #1 finished! INFO @ Tue, 02 Aug 2022 15:07:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:07:28: #2 number of paired peaks: 825 WARNING @ Tue, 02 Aug 2022 15:07:28: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Tue, 02 Aug 2022 15:07:28: start model_add_line... INFO @ Tue, 02 Aug 2022 15:07:28: start X-correlation... INFO @ Tue, 02 Aug 2022 15:07:28: end of X-cor INFO @ Tue, 02 Aug 2022 15:07:28: #2 finished! INFO @ Tue, 02 Aug 2022 15:07:28: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 15:07:28: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 15:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.20_model.r WARNING @ Tue, 02 Aug 2022 15:07:29: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:07:29: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 15:07:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:07:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:07:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:07:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206490/SRX15206490.20_summits.bed INFO @ Tue, 02 Aug 2022 15:07:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 95 millis CompletedMACS2peakCalling