Job ID = 16437610 SRX = ERX5847888 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T03:57:30 prefetch.2.10.7: 1) Downloading 'ERR6212898'... 2022-08-02T03:57:30 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:57:42 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:57:42 prefetch.2.10.7: 'ERR6212898' is valid 2022-08-02T03:57:42 prefetch.2.10.7: 1) 'ERR6212898' was downloaded successfully 2022-08-02T03:57:42 prefetch.2.10.7: 'ERR6212898' has 0 unresolved dependencies Read 4569501 spots for ERR6212898/ERR6212898.sra Written 4569501 spots for ERR6212898/ERR6212898.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437874 ("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: 00:05:17 4569501 reads; of these: 4569501 (100.00%) were paired; of these: 247820 (5.42%) aligned concordantly 0 times 3670449 (80.32%) aligned concordantly exactly 1 time 651232 (14.25%) aligned concordantly >1 times ---- 247820 pairs aligned concordantly 0 times; of these: 14455 (5.83%) aligned discordantly 1 time ---- 233365 pairs aligned 0 times concordantly or discordantly; of these: 466730 mates make up the pairs; of these: 314148 (67.31%) aligned 0 times 126873 (27.18%) aligned exactly 1 time 25709 (5.51%) aligned >1 times 96.56% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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_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] 33948 / 4334078 = 0.0078 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 13:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.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 13:05:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:05:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:05:59: 1000000 INFO @ Tue, 02 Aug 2022 13:06:05: 2000000 INFO @ Tue, 02 Aug 2022 13:06:11: 3000000 INFO @ Tue, 02 Aug 2022 13:06:18: 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 13:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.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 13:06:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:06:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:06:24: 5000000 INFO @ Tue, 02 Aug 2022 13:06:29: 1000000 INFO @ Tue, 02 Aug 2022 13:06:30: 6000000 INFO @ Tue, 02 Aug 2022 13:06:36: 2000000 INFO @ Tue, 02 Aug 2022 13:06:37: 7000000 INFO @ Tue, 02 Aug 2022 13:06:43: 3000000 INFO @ Tue, 02 Aug 2022 13:06:44: 8000000 INFO @ Tue, 02 Aug 2022 13:06:49: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 13:06:49: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 13:06:49: #1 total tags in treatment: 4287764 INFO @ Tue, 02 Aug 2022 13:06:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:06:49: #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 13:06:49: #1 tags after filtering in treatment: 4215101 INFO @ Tue, 02 Aug 2022 13:06:49: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:06:49: #1 finished! INFO @ Tue, 02 Aug 2022 13:06:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:06:49: #2 number of paired peaks: 114 WARNING @ Tue, 02 Aug 2022 13:06:49: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 02 Aug 2022 13:06:49: start model_add_line... INFO @ Tue, 02 Aug 2022 13:06:49: start X-correlation... INFO @ Tue, 02 Aug 2022 13:06:50: end of X-cor INFO @ Tue, 02 Aug 2022 13:06:50: #2 finished! INFO @ Tue, 02 Aug 2022 13:06:50: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 13:06:50: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 13:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.05_model.r WARNING @ Tue, 02 Aug 2022 13:06:50: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:06:50: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 13:06:50: #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 13:06:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:06:50: 4000000 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 13:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.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 13:06:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:06:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:06:56: 5000000 INFO @ Tue, 02 Aug 2022 13:06:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:06:59: 1000000 INFO @ Tue, 02 Aug 2022 13:07:03: 6000000 INFO @ Tue, 02 Aug 2022 13:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:07:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.05_summits.bed INFO @ Tue, 02 Aug 2022 13:07:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 73 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:07:06: 2000000 INFO @ Tue, 02 Aug 2022 13:07:09: 7000000 INFO @ Tue, 02 Aug 2022 13:07:13: 3000000 INFO @ Tue, 02 Aug 2022 13:07:16: 8000000 INFO @ Tue, 02 Aug 2022 13:07:19: 4000000 INFO @ Tue, 02 Aug 2022 13:07:20: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 13:07:20: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 13:07:20: #1 total tags in treatment: 4287764 INFO @ Tue, 02 Aug 2022 13:07:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:07:20: #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 13:07:21: #1 tags after filtering in treatment: 4215101 INFO @ Tue, 02 Aug 2022 13:07:21: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:07:21: #1 finished! INFO @ Tue, 02 Aug 2022 13:07:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:07:21: #2 number of paired peaks: 114 WARNING @ Tue, 02 Aug 2022 13:07:21: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 02 Aug 2022 13:07:21: start model_add_line... INFO @ Tue, 02 Aug 2022 13:07:21: start X-correlation... INFO @ Tue, 02 Aug 2022 13:07:21: end of X-cor INFO @ Tue, 02 Aug 2022 13:07:21: #2 finished! INFO @ Tue, 02 Aug 2022 13:07:21: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 13:07:21: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 13:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.10_model.r WARNING @ Tue, 02 Aug 2022 13:07:21: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:07:21: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 13:07:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:07:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:07:26: 5000000 INFO @ Tue, 02 Aug 2022 13:07:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:07:31: 6000000 INFO @ Tue, 02 Aug 2022 13:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:07:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:07:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.10_summits.bed INFO @ Tue, 02 Aug 2022 13:07:35: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:07:37: 7000000 INFO @ Tue, 02 Aug 2022 13:07:43: 8000000 INFO @ Tue, 02 Aug 2022 13:07:48: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 13:07:48: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 13:07:48: #1 total tags in treatment: 4287764 INFO @ Tue, 02 Aug 2022 13:07:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:07:48: #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 13:07:48: #1 tags after filtering in treatment: 4215101 INFO @ Tue, 02 Aug 2022 13:07:48: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:07:48: #1 finished! INFO @ Tue, 02 Aug 2022 13:07:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:07:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:07:48: #2 number of paired peaks: 114 WARNING @ Tue, 02 Aug 2022 13:07:48: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 02 Aug 2022 13:07:48: start model_add_line... INFO @ Tue, 02 Aug 2022 13:07:48: start X-correlation... INFO @ Tue, 02 Aug 2022 13:07:48: end of X-cor INFO @ Tue, 02 Aug 2022 13:07:48: #2 finished! INFO @ Tue, 02 Aug 2022 13:07:48: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 13:07:48: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 13:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.20_model.r WARNING @ Tue, 02 Aug 2022 13:07:48: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:07:48: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 13:07:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:07:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:07:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:07:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847888/ERX5847888.20_summits.bed INFO @ Tue, 02 Aug 2022 13:08:02: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (58 records, 4 fields): 21 millis CompletedMACS2peakCalling