Job ID = 16439429 SRX = SRX11245085 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:08:54 prefetch.2.10.7: 1) Downloading 'SRR14932350'... 2022-08-02T06:08:54 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:09:24 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:09:24 prefetch.2.10.7: 1) 'SRR14932350' was downloaded successfully 2022-08-02T06:09:24 prefetch.2.10.7: 'SRR14932350' has 0 unresolved dependencies Read 15043121 spots for SRR14932350/SRR14932350.sra Written 15043121 spots for SRR14932350/SRR14932350.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439628 ("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: 00:30:04 15043121 reads; of these: 15043121 (100.00%) were paired; of these: 8700975 (57.84%) aligned concordantly 0 times 5085264 (33.80%) aligned concordantly exactly 1 time 1256882 (8.36%) aligned concordantly >1 times ---- 8700975 pairs aligned concordantly 0 times; of these: 1031734 (11.86%) aligned discordantly 1 time ---- 7669241 pairs aligned 0 times concordantly or discordantly; of these: 15338482 mates make up the pairs; of these: 14533688 (94.75%) aligned 0 times 270924 (1.77%) aligned exactly 1 time 533870 (3.48%) aligned >1 times 51.69% overall alignment rate Time searching: 00:30:04 Overall time: 00:30:04 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 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2595651 / 7348929 = 0.3532 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 15:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.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 15:46:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:46:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:46:37: 1000000 INFO @ Tue, 02 Aug 2022 15:46:43: 2000000 INFO @ Tue, 02 Aug 2022 15:46:49: 3000000 INFO @ Tue, 02 Aug 2022 15:46:56: 4000000 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 15:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.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 15:46:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:46:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:47:02: 5000000 INFO @ Tue, 02 Aug 2022 15:47:07: 1000000 INFO @ Tue, 02 Aug 2022 15:47:09: 6000000 INFO @ Tue, 02 Aug 2022 15:47:15: 2000000 INFO @ Tue, 02 Aug 2022 15:47:15: 7000000 INFO @ Tue, 02 Aug 2022 15:47:22: 8000000 INFO @ Tue, 02 Aug 2022 15:47:23: 3000000 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 15:47:29: 9000000 INFO @ Tue, 02 Aug 2022 15:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.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 15:47:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:47:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:47:31: 4000000 INFO @ Tue, 02 Aug 2022 15:47:36: 10000000 INFO @ Tue, 02 Aug 2022 15:47:37: 1000000 INFO @ Tue, 02 Aug 2022 15:47:39: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:47:39: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:47:39: #1 total tags in treatment: 4125420 INFO @ Tue, 02 Aug 2022 15:47:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:47:39: #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 15:47:39: #1 tags after filtering in treatment: 3995455 INFO @ Tue, 02 Aug 2022 15:47:39: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:47:39: #1 finished! INFO @ Tue, 02 Aug 2022 15:47:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:47:39: #2 number of paired peaks: 315 WARNING @ Tue, 02 Aug 2022 15:47:39: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 02 Aug 2022 15:47:39: start model_add_line... INFO @ Tue, 02 Aug 2022 15:47:39: start X-correlation... INFO @ Tue, 02 Aug 2022 15:47:39: end of X-cor INFO @ Tue, 02 Aug 2022 15:47:39: #2 finished! INFO @ Tue, 02 Aug 2022 15:47:39: #2 predicted fragment length is 184 bps INFO @ Tue, 02 Aug 2022 15:47:39: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 02 Aug 2022 15:47:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.05_model.r WARNING @ Tue, 02 Aug 2022 15:47:39: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:47:39: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Tue, 02 Aug 2022 15:47:39: #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 15:47:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:47:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:47:39: 5000000 INFO @ Tue, 02 Aug 2022 15:47:43: 2000000 INFO @ Tue, 02 Aug 2022 15:47:47: 6000000 INFO @ Tue, 02 Aug 2022 15:47:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:47:49: 3000000 INFO @ Tue, 02 Aug 2022 15:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.05_summits.bed INFO @ Tue, 02 Aug 2022 15:47:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (788 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:47:55: 7000000 INFO @ Tue, 02 Aug 2022 15:47:56: 4000000 INFO @ Tue, 02 Aug 2022 15:48:02: 5000000 INFO @ Tue, 02 Aug 2022 15:48:03: 8000000 INFO @ Tue, 02 Aug 2022 15:48:08: 6000000 INFO @ Tue, 02 Aug 2022 15:48:11: 9000000 INFO @ Tue, 02 Aug 2022 15:48:15: 7000000 INFO @ Tue, 02 Aug 2022 15:48:19: 10000000 INFO @ Tue, 02 Aug 2022 15:48:21: 8000000 INFO @ Tue, 02 Aug 2022 15:48:22: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:48:22: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:48:22: #1 total tags in treatment: 4125420 INFO @ Tue, 02 Aug 2022 15:48:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:48:22: #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 15:48:22: #1 tags after filtering in treatment: 3995455 INFO @ Tue, 02 Aug 2022 15:48:22: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:48:22: #1 finished! INFO @ Tue, 02 Aug 2022 15:48:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:48:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:48:23: #2 number of paired peaks: 315 WARNING @ Tue, 02 Aug 2022 15:48:23: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 02 Aug 2022 15:48:23: start model_add_line... INFO @ Tue, 02 Aug 2022 15:48:23: start X-correlation... INFO @ Tue, 02 Aug 2022 15:48:23: end of X-cor INFO @ Tue, 02 Aug 2022 15:48:23: #2 finished! INFO @ Tue, 02 Aug 2022 15:48:23: #2 predicted fragment length is 184 bps INFO @ Tue, 02 Aug 2022 15:48:23: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 02 Aug 2022 15:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.10_model.r WARNING @ Tue, 02 Aug 2022 15:48:23: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:48:23: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Tue, 02 Aug 2022 15:48:23: #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 15:48:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:48:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:48:28: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:48:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:48:34: 10000000 INFO @ Tue, 02 Aug 2022 15:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.10_summits.bed INFO @ Tue, 02 Aug 2022 15:48:36: Done! INFO @ Tue, 02 Aug 2022 15:48:36: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:48:36: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:48:36: #1 total tags in treatment: 4125420 INFO @ Tue, 02 Aug 2022 15:48:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:48:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (14 chroms): 1 millis INFO @ Tue, 02 Aug 2022 15:48:36: #1 tags after filtering in treatment: 3995455 INFO @ Tue, 02 Aug 2022 15:48:36: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:48:36: #1 finished! INFO @ Tue, 02 Aug 2022 15:48:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:48:36: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (527 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:48:37: #2 number of paired peaks: 315 WARNING @ Tue, 02 Aug 2022 15:48:37: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 02 Aug 2022 15:48:37: start model_add_line... INFO @ Tue, 02 Aug 2022 15:48:37: start X-correlation... INFO @ Tue, 02 Aug 2022 15:48:37: end of X-cor INFO @ Tue, 02 Aug 2022 15:48:37: #2 finished! INFO @ Tue, 02 Aug 2022 15:48:37: #2 predicted fragment length is 184 bps INFO @ Tue, 02 Aug 2022 15:48:37: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 02 Aug 2022 15:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.20_model.r WARNING @ Tue, 02 Aug 2022 15:48:37: #2 Since the d (184) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:48:37: #2 You may need to consider one of the other alternative d(s): 184 WARNING @ Tue, 02 Aug 2022 15:48:37: #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 15:48:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:48:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245085/SRX11245085.20_summits.bed INFO @ Tue, 02 Aug 2022 15:48:50: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (336 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。