Job ID = 16440171 SRX = SRX15369005 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T08:28:16 prefetch.2.10.7: 1) Downloading 'SRR19308734'... 2022-08-02T08:28:16 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T08:29:18 prefetch.2.10.7: HTTPS download succeed 2022-08-02T08:29:18 prefetch.2.10.7: 1) 'SRR19308734' was downloaded successfully 2022-08-02T08:29:18 prefetch.2.10.7: 'SRR19308734' has 0 unresolved dependencies Read 29920566 spots for SRR19308734/SRR19308734.sra Written 29920566 spots for SRR19308734/SRR19308734.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440767 ("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: 00:16:30 29920566 reads; of these: 29920566 (100.00%) were unpaired; of these: 1027524 (3.43%) aligned 0 times 19849709 (66.34%) aligned exactly 1 time 9043333 (30.22%) aligned >1 times 96.57% overall alignment rate Time searching: 00:16:31 Overall time: 00:16:31 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_rmdupse_core] 10634456 / 28893042 = 0.3681 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 17:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.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 17:55:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:55:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:55:13: 1000000 INFO @ Tue, 02 Aug 2022 17:55:19: 2000000 INFO @ Tue, 02 Aug 2022 17:55:26: 3000000 INFO @ Tue, 02 Aug 2022 17:55:33: 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 17:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.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 17:55:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:55:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:55:40: 5000000 INFO @ Tue, 02 Aug 2022 17:55:43: 1000000 INFO @ Tue, 02 Aug 2022 17:55:47: 6000000 INFO @ Tue, 02 Aug 2022 17:55:50: 2000000 INFO @ Tue, 02 Aug 2022 17:55:55: 7000000 INFO @ Tue, 02 Aug 2022 17:55:58: 3000000 INFO @ Tue, 02 Aug 2022 17:56:03: 8000000 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 17:56:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.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 17:56:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:56:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:56:05: 4000000 INFO @ Tue, 02 Aug 2022 17:56:11: 9000000 INFO @ Tue, 02 Aug 2022 17:56:13: 5000000 INFO @ Tue, 02 Aug 2022 17:56:13: 1000000 INFO @ Tue, 02 Aug 2022 17:56:18: 10000000 INFO @ Tue, 02 Aug 2022 17:56:20: 6000000 INFO @ Tue, 02 Aug 2022 17:56:20: 2000000 INFO @ Tue, 02 Aug 2022 17:56:26: 11000000 INFO @ Tue, 02 Aug 2022 17:56:28: 7000000 INFO @ Tue, 02 Aug 2022 17:56:28: 3000000 INFO @ Tue, 02 Aug 2022 17:56:34: 12000000 INFO @ Tue, 02 Aug 2022 17:56:35: 4000000 INFO @ Tue, 02 Aug 2022 17:56:36: 8000000 INFO @ Tue, 02 Aug 2022 17:56:42: 13000000 INFO @ Tue, 02 Aug 2022 17:56:43: 5000000 INFO @ Tue, 02 Aug 2022 17:56:44: 9000000 INFO @ Tue, 02 Aug 2022 17:56:50: 14000000 INFO @ Tue, 02 Aug 2022 17:56:51: 6000000 INFO @ Tue, 02 Aug 2022 17:56:52: 10000000 INFO @ Tue, 02 Aug 2022 17:56:58: 15000000 INFO @ Tue, 02 Aug 2022 17:56:58: 7000000 INFO @ Tue, 02 Aug 2022 17:57:00: 11000000 INFO @ Tue, 02 Aug 2022 17:57:06: 16000000 INFO @ Tue, 02 Aug 2022 17:57:06: 8000000 INFO @ Tue, 02 Aug 2022 17:57:08: 12000000 INFO @ Tue, 02 Aug 2022 17:57:14: 17000000 INFO @ Tue, 02 Aug 2022 17:57:14: 9000000 INFO @ Tue, 02 Aug 2022 17:57:16: 13000000 INFO @ Tue, 02 Aug 2022 17:57:22: 18000000 INFO @ Tue, 02 Aug 2022 17:57:23: 10000000 INFO @ Tue, 02 Aug 2022 17:57:24: 14000000 INFO @ Tue, 02 Aug 2022 17:57:24: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:57:24: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:57:24: #1 total tags in treatment: 18258586 INFO @ Tue, 02 Aug 2022 17:57:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:57:24: #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 17:57:24: #1 tags after filtering in treatment: 18258586 INFO @ Tue, 02 Aug 2022 17:57:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:57:24: #1 finished! INFO @ Tue, 02 Aug 2022 17:57:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:57:25: #2 number of paired peaks: 236 WARNING @ Tue, 02 Aug 2022 17:57:25: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 02 Aug 2022 17:57:25: start model_add_line... INFO @ Tue, 02 Aug 2022 17:57:25: start X-correlation... INFO @ Tue, 02 Aug 2022 17:57:26: end of X-cor INFO @ Tue, 02 Aug 2022 17:57:26: #2 finished! INFO @ Tue, 02 Aug 2022 17:57:26: #2 predicted fragment length is 138 bps INFO @ Tue, 02 Aug 2022 17:57:26: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 02 Aug 2022 17:57:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.05_model.r WARNING @ Tue, 02 Aug 2022 17:57:26: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:57:26: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Tue, 02 Aug 2022 17:57:26: #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 17:57:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:57:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:57:31: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:57:32: 15000000 INFO @ Tue, 02 Aug 2022 17:57:39: 12000000 INFO @ Tue, 02 Aug 2022 17:57:40: 16000000 INFO @ Tue, 02 Aug 2022 17:57:47: 13000000 INFO @ Tue, 02 Aug 2022 17:57:48: 17000000 INFO @ Tue, 02 Aug 2022 17:57:55: 14000000 INFO @ Tue, 02 Aug 2022 17:57:56: 18000000 INFO @ Tue, 02 Aug 2022 17:57:58: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:57:58: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:57:58: #1 total tags in treatment: 18258586 INFO @ Tue, 02 Aug 2022 17:57:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:57:58: #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 17:57:58: #1 tags after filtering in treatment: 18258586 INFO @ Tue, 02 Aug 2022 17:57:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:57:58: #1 finished! INFO @ Tue, 02 Aug 2022 17:57:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:57:59: #2 number of paired peaks: 236 WARNING @ Tue, 02 Aug 2022 17:57:59: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 02 Aug 2022 17:57:59: start model_add_line... INFO @ Tue, 02 Aug 2022 17:57:59: start X-correlation... INFO @ Tue, 02 Aug 2022 17:57:59: end of X-cor INFO @ Tue, 02 Aug 2022 17:57:59: #2 finished! INFO @ Tue, 02 Aug 2022 17:57:59: #2 predicted fragment length is 138 bps INFO @ Tue, 02 Aug 2022 17:57:59: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 02 Aug 2022 17:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.10_model.r WARNING @ Tue, 02 Aug 2022 17:57:59: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:57:59: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Tue, 02 Aug 2022 17:57:59: #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 17:57:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:57:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:58:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:58:02: 15000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:58:10: 16000000 INFO @ Tue, 02 Aug 2022 17:58:17: 17000000 INFO @ Tue, 02 Aug 2022 17:58:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:58:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:58:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.05_summits.bed INFO @ Tue, 02 Aug 2022 17:58:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (13187 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:58:25: 18000000 INFO @ Tue, 02 Aug 2022 17:58:27: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:58:27: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:58:27: #1 total tags in treatment: 18258586 INFO @ Tue, 02 Aug 2022 17:58:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:58:27: #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 17:58:27: #1 tags after filtering in treatment: 18258586 INFO @ Tue, 02 Aug 2022 17:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:58:27: #1 finished! INFO @ Tue, 02 Aug 2022 17:58:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:58:28: #2 number of paired peaks: 236 WARNING @ Tue, 02 Aug 2022 17:58:28: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 02 Aug 2022 17:58:28: start model_add_line... INFO @ Tue, 02 Aug 2022 17:58:28: start X-correlation... INFO @ Tue, 02 Aug 2022 17:58:28: end of X-cor INFO @ Tue, 02 Aug 2022 17:58:28: #2 finished! INFO @ Tue, 02 Aug 2022 17:58:28: #2 predicted fragment length is 138 bps INFO @ Tue, 02 Aug 2022 17:58:28: #2 alternative fragment length(s) may be 138 bps INFO @ Tue, 02 Aug 2022 17:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.20_model.r WARNING @ Tue, 02 Aug 2022 17:58:28: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:58:28: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Tue, 02 Aug 2022 17:58:28: #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 17:58:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:58:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.10_summits.bed INFO @ Tue, 02 Aug 2022 17:58:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7587 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:59:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369005/SRX15369005.20_summits.bed INFO @ Tue, 02 Aug 2022 17:59:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2972 records, 4 fields): 42 millis CompletedMACS2peakCalling