Job ID = 16439128 SRX = SRX15206450 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:34:31 prefetch.2.10.7: 1) Downloading 'SRR19139357'... 2022-08-02T05:34:31 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:34:56 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:34:57 prefetch.2.10.7: 'SRR19139357' is valid 2022-08-02T05:34:57 prefetch.2.10.7: 1) 'SRR19139357' was downloaded successfully 2022-08-02T05:34:57 prefetch.2.10.7: 'SRR19139357' has 0 unresolved dependencies Read 23843646 spots for SRR19139357/SRR19139357.sra Written 23843646 spots for SRR19139357/SRR19139357.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439181 ("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: 00:06:13 23843646 reads; of these: 23843646 (100.00%) were unpaired; of these: 720050 (3.02%) aligned 0 times 19610661 (82.25%) aligned exactly 1 time 3512935 (14.73%) aligned >1 times 96.98% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 1723059 / 23123596 = 0.0745 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 14:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.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 14:46:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:46:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:46:50: 1000000 INFO @ Tue, 02 Aug 2022 14:46:55: 2000000 INFO @ Tue, 02 Aug 2022 14:47:01: 3000000 INFO @ Tue, 02 Aug 2022 14:47:06: 4000000 INFO @ Tue, 02 Aug 2022 14:47:11: 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 14:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.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 14:47:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:47:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:47:16: 6000000 INFO @ Tue, 02 Aug 2022 14:47:20: 1000000 INFO @ Tue, 02 Aug 2022 14:47:21: 7000000 INFO @ Tue, 02 Aug 2022 14:47:26: 2000000 INFO @ Tue, 02 Aug 2022 14:47:27: 8000000 INFO @ Tue, 02 Aug 2022 14:47:31: 3000000 INFO @ Tue, 02 Aug 2022 14:47:32: 9000000 INFO @ Tue, 02 Aug 2022 14:47:37: 4000000 INFO @ Tue, 02 Aug 2022 14:47:37: 10000000 INFO @ Tue, 02 Aug 2022 14:47:42: 5000000 INFO @ Tue, 02 Aug 2022 14:47:42: 11000000 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 14:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.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 14:47:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:47:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:47:47: 6000000 INFO @ Tue, 02 Aug 2022 14:47:47: 12000000 INFO @ Tue, 02 Aug 2022 14:47:50: 1000000 INFO @ Tue, 02 Aug 2022 14:47:52: 7000000 INFO @ Tue, 02 Aug 2022 14:47:53: 13000000 INFO @ Tue, 02 Aug 2022 14:47:56: 2000000 INFO @ Tue, 02 Aug 2022 14:47:57: 8000000 INFO @ Tue, 02 Aug 2022 14:47:58: 14000000 INFO @ Tue, 02 Aug 2022 14:48:01: 3000000 INFO @ Tue, 02 Aug 2022 14:48:02: 9000000 INFO @ Tue, 02 Aug 2022 14:48:03: 15000000 INFO @ Tue, 02 Aug 2022 14:48:06: 4000000 INFO @ Tue, 02 Aug 2022 14:48:08: 10000000 INFO @ Tue, 02 Aug 2022 14:48:08: 16000000 INFO @ Tue, 02 Aug 2022 14:48:11: 5000000 INFO @ Tue, 02 Aug 2022 14:48:13: 11000000 INFO @ Tue, 02 Aug 2022 14:48:14: 17000000 INFO @ Tue, 02 Aug 2022 14:48:15: 6000000 INFO @ Tue, 02 Aug 2022 14:48:18: 12000000 INFO @ Tue, 02 Aug 2022 14:48:19: 18000000 INFO @ Tue, 02 Aug 2022 14:48:20: 7000000 INFO @ Tue, 02 Aug 2022 14:48:23: 13000000 INFO @ Tue, 02 Aug 2022 14:48:25: 19000000 INFO @ Tue, 02 Aug 2022 14:48:25: 8000000 INFO @ Tue, 02 Aug 2022 14:48:29: 14000000 INFO @ Tue, 02 Aug 2022 14:48:30: 9000000 INFO @ Tue, 02 Aug 2022 14:48:30: 20000000 INFO @ Tue, 02 Aug 2022 14:48:34: 15000000 INFO @ Tue, 02 Aug 2022 14:48:34: 10000000 INFO @ Tue, 02 Aug 2022 14:48:35: 21000000 INFO @ Tue, 02 Aug 2022 14:48:37: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:48:37: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:48:37: #1 total tags in treatment: 21400537 INFO @ Tue, 02 Aug 2022 14:48:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:37: #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 14:48:37: #1 tags after filtering in treatment: 21400537 INFO @ Tue, 02 Aug 2022 14:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:37: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:39: #2 number of paired peaks: 102 WARNING @ Tue, 02 Aug 2022 14:48:39: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 02 Aug 2022 14:48:39: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:39: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:39: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:39: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:39: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 14:48:39: #2 alternative fragment length(s) may be 3,55,107,126,163,182,214,384,466,495,556,593 bps INFO @ Tue, 02 Aug 2022 14:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.05_model.r WARNING @ Tue, 02 Aug 2022 14:48:39: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:48:39: #2 You may need to consider one of the other alternative d(s): 3,55,107,126,163,182,214,384,466,495,556,593 WARNING @ Tue, 02 Aug 2022 14:48:39: #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 14:48:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:48:39: 11000000 INFO @ Tue, 02 Aug 2022 14:48:39: 16000000 INFO @ Tue, 02 Aug 2022 14:48:44: 12000000 INFO @ Tue, 02 Aug 2022 14:48:44: 17000000 INFO @ Tue, 02 Aug 2022 14:48:49: 13000000 INFO @ Tue, 02 Aug 2022 14:48:50: 18000000 INFO @ Tue, 02 Aug 2022 14:48:53: 14000000 INFO @ Tue, 02 Aug 2022 14:48:55: 19000000 INFO @ Tue, 02 Aug 2022 14:48:58: 15000000 INFO @ Tue, 02 Aug 2022 14:49:00: 20000000 INFO @ Tue, 02 Aug 2022 14:49:03: 16000000 INFO @ Tue, 02 Aug 2022 14:49:05: 21000000 INFO @ Tue, 02 Aug 2022 14:49:07: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:49:07: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:49:07: #1 total tags in treatment: 21400537 INFO @ Tue, 02 Aug 2022 14:49:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:07: #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 14:49:08: 17000000 INFO @ Tue, 02 Aug 2022 14:49:08: #1 tags after filtering in treatment: 21400537 INFO @ Tue, 02 Aug 2022 14:49:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:08: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:09: #2 number of paired peaks: 102 WARNING @ Tue, 02 Aug 2022 14:49:09: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 02 Aug 2022 14:49:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:09: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:09: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:09: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:09: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 14:49:09: #2 alternative fragment length(s) may be 3,55,107,126,163,182,214,384,466,495,556,593 bps INFO @ Tue, 02 Aug 2022 14:49:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.10_model.r WARNING @ Tue, 02 Aug 2022 14:49:09: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:49:09: #2 You may need to consider one of the other alternative d(s): 3,55,107,126,163,182,214,384,466,495,556,593 WARNING @ Tue, 02 Aug 2022 14:49:09: #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 14:49:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:49:12: 18000000 INFO @ Tue, 02 Aug 2022 14:49:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:49:17: 19000000 INFO @ Tue, 02 Aug 2022 14:49:21: 20000000 INFO @ Tue, 02 Aug 2022 14:49:26: 21000000 INFO @ Tue, 02 Aug 2022 14:49:28: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:49:28: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:49:28: #1 total tags in treatment: 21400537 INFO @ Tue, 02 Aug 2022 14:49:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:28: #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 14:49:28: #1 tags after filtering in treatment: 21400537 INFO @ Tue, 02 Aug 2022 14:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:28: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:29: #2 number of paired peaks: 102 WARNING @ Tue, 02 Aug 2022 14:49:29: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 02 Aug 2022 14:49:29: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:29: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:29: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:29: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:29: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 14:49:29: #2 alternative fragment length(s) may be 3,55,107,126,163,182,214,384,466,495,556,593 bps INFO @ Tue, 02 Aug 2022 14:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.20_model.r WARNING @ Tue, 02 Aug 2022 14:49:29: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:49:29: #2 You may need to consider one of the other alternative d(s): 3,55,107,126,163,182,214,384,466,495,556,593 WARNING @ Tue, 02 Aug 2022 14:49:29: #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 14:49:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.05_summits.bed INFO @ Tue, 02 Aug 2022 14:49:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (105 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:49:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.10_summits.bed INFO @ Tue, 02 Aug 2022 14:50:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206450/SRX15206450.20_summits.bed INFO @ Tue, 02 Aug 2022 14:50:26: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 15 millis CompletedMACS2peakCalling