Job ID = 16439437 SRX = SRX11965416 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T06:10:12 prefetch.2.10.7: 1) Downloading 'SRR15668751'... 2022-08-02T06:10:12 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:10:29 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:10:30 prefetch.2.10.7: 'SRR15668751' is valid 2022-08-02T06:10:30 prefetch.2.10.7: 1) 'SRR15668751' was downloaded successfully 2022-08-02T06:10:30 prefetch.2.10.7: 'SRR15668751' has 0 unresolved dependencies Read 12783633 spots for SRR15668751/SRR15668751.sra Written 12783633 spots for SRR15668751/SRR15668751.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439474 ("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: 00:03:50 12783633 reads; of these: 12783633 (100.00%) were unpaired; of these: 581214 (4.55%) aligned 0 times 10076344 (78.82%) aligned exactly 1 time 2126075 (16.63%) aligned >1 times 95.45% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 2467877 / 12202419 = 0.2022 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 15:17:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.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 15:17:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:17:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:17:54: 1000000 INFO @ Tue, 02 Aug 2022 15:17:59: 2000000 INFO @ Tue, 02 Aug 2022 15:18:04: 3000000 INFO @ Tue, 02 Aug 2022 15:18:09: 4000000 INFO @ Tue, 02 Aug 2022 15:18:14: 5000000 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 15:18:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.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 15:18:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:18:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:18:19: 6000000 INFO @ Tue, 02 Aug 2022 15:18:23: 1000000 INFO @ Tue, 02 Aug 2022 15:18:24: 7000000 INFO @ Tue, 02 Aug 2022 15:18:29: 8000000 INFO @ Tue, 02 Aug 2022 15:18:29: 2000000 INFO @ Tue, 02 Aug 2022 15:18:34: 9000000 INFO @ Tue, 02 Aug 2022 15:18:35: 3000000 INFO @ Tue, 02 Aug 2022 15:18:38: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:18:38: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:18:38: #1 total tags in treatment: 9734542 INFO @ Tue, 02 Aug 2022 15:18:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:18:38: #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 15:18:38: #1 tags after filtering in treatment: 9734542 INFO @ Tue, 02 Aug 2022 15:18:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:18:38: #1 finished! INFO @ Tue, 02 Aug 2022 15:18:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:18:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:18:39: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 15:18:39: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 15:18:39: start model_add_line... INFO @ Tue, 02 Aug 2022 15:18:39: start X-correlation... INFO @ Tue, 02 Aug 2022 15:18:39: end of X-cor INFO @ Tue, 02 Aug 2022 15:18:39: #2 finished! INFO @ Tue, 02 Aug 2022 15:18:39: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 15:18:39: #2 alternative fragment length(s) may be 2,49,339,502,534 bps INFO @ Tue, 02 Aug 2022 15:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.05_model.r WARNING @ Tue, 02 Aug 2022 15:18:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:18:39: #2 You may need to consider one of the other alternative d(s): 2,49,339,502,534 WARNING @ Tue, 02 Aug 2022 15:18:39: #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 15:18:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:18:40: 4000000 INFO @ Tue, 02 Aug 2022 15:18:45: 5000000 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 15:18:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.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 15:18:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:18:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:18:50: 6000000 INFO @ Tue, 02 Aug 2022 15:18:53: 1000000 INFO @ Tue, 02 Aug 2022 15:18:55: 7000000 INFO @ Tue, 02 Aug 2022 15:18:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:59: 2000000 INFO @ Tue, 02 Aug 2022 15:19:00: 8000000 INFO @ Tue, 02 Aug 2022 15:19:05: 3000000 INFO @ Tue, 02 Aug 2022 15:19:06: 9000000 INFO @ Tue, 02 Aug 2022 15:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.05_summits.bed INFO @ Tue, 02 Aug 2022 15:19:09: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:19:09: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:19:09: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:19:09: #1 total tags in treatment: 9734542 INFO @ Tue, 02 Aug 2022 15:19:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:19:09: #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 15:19:10: #1 tags after filtering in treatment: 9734542 INFO @ Tue, 02 Aug 2022 15:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:19:10: #1 finished! INFO @ Tue, 02 Aug 2022 15:19:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:19:10: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 15:19:10: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 15:19:10: start model_add_line... INFO @ Tue, 02 Aug 2022 15:19:10: start X-correlation... INFO @ Tue, 02 Aug 2022 15:19:11: 4000000 INFO @ Tue, 02 Aug 2022 15:19:11: end of X-cor INFO @ Tue, 02 Aug 2022 15:19:11: #2 finished! INFO @ Tue, 02 Aug 2022 15:19:11: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 15:19:11: #2 alternative fragment length(s) may be 2,49,339,502,534 bps INFO @ Tue, 02 Aug 2022 15:19:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.10_model.r WARNING @ Tue, 02 Aug 2022 15:19:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:19:11: #2 You may need to consider one of the other alternative d(s): 2,49,339,502,534 WARNING @ Tue, 02 Aug 2022 15:19:11: #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 15:19:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:19:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:19:16: 5000000 INFO @ Tue, 02 Aug 2022 15:19:22: 6000000 INFO @ Tue, 02 Aug 2022 15:19:28: 7000000 INFO @ Tue, 02 Aug 2022 15:19:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:19:33: 8000000 INFO @ Tue, 02 Aug 2022 15:19:39: 9000000 INFO @ Tue, 02 Aug 2022 15:19:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:19:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:19:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.10_summits.bed INFO @ Tue, 02 Aug 2022 15:19:40: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:19:43: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:19:43: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:19:43: #1 total tags in treatment: 9734542 INFO @ Tue, 02 Aug 2022 15:19:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:19:43: #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 15:19:43: #1 tags after filtering in treatment: 9734542 INFO @ Tue, 02 Aug 2022 15:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:19:43: #1 finished! INFO @ Tue, 02 Aug 2022 15:19:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:19:44: #2 number of paired peaks: 104 WARNING @ Tue, 02 Aug 2022 15:19:44: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 02 Aug 2022 15:19:44: start model_add_line... INFO @ Tue, 02 Aug 2022 15:19:44: start X-correlation... INFO @ Tue, 02 Aug 2022 15:19:44: end of X-cor INFO @ Tue, 02 Aug 2022 15:19:44: #2 finished! INFO @ Tue, 02 Aug 2022 15:19:44: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 15:19:44: #2 alternative fragment length(s) may be 2,49,339,502,534 bps INFO @ Tue, 02 Aug 2022 15:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.20_model.r WARNING @ Tue, 02 Aug 2022 15:19:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:19:44: #2 You may need to consider one of the other alternative d(s): 2,49,339,502,534 WARNING @ Tue, 02 Aug 2022 15:19:44: #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 15:19:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:19:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:20:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11965416/SRX11965416.20_summits.bed INFO @ Tue, 02 Aug 2022 15:20:14: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 52 millis CompletedMACS2peakCalling