Job ID = 16440185 SRX = SRX15369006 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T08:30:24 prefetch.2.10.7: 1) Downloading 'SRR19308735'... 2022-08-02T08:30:24 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T08:31:00 prefetch.2.10.7: HTTPS download succeed 2022-08-02T08:31:00 prefetch.2.10.7: 1) 'SRR19308735' was downloaded successfully 2022-08-02T08:31:00 prefetch.2.10.7: 'SRR19308735' has 0 unresolved dependencies Read 17539494 spots for SRR19308735/SRR19308735.sra Written 17539494 spots for SRR19308735/SRR19308735.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440719 ("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: 00:11:06 17539494 reads; of these: 17539494 (100.00%) were unpaired; of these: 634646 (3.62%) aligned 0 times 9745480 (55.56%) aligned exactly 1 time 7159368 (40.82%) aligned >1 times 96.38% overall alignment rate Time searching: 00:11:07 Overall time: 00:11:07 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] 3941785 / 16904848 = 0.2332 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 17:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.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 17:48:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:48:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:48:15: 1000000 INFO @ Tue, 02 Aug 2022 17:48:21: 2000000 INFO @ Tue, 02 Aug 2022 17:48:28: 3000000 INFO @ Tue, 02 Aug 2022 17:48:34: 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 17:48:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.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 17:48:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:48:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:48:40: 5000000 INFO @ Tue, 02 Aug 2022 17:48:45: 1000000 INFO @ Tue, 02 Aug 2022 17:48:47: 6000000 INFO @ Tue, 02 Aug 2022 17:48:51: 2000000 INFO @ Tue, 02 Aug 2022 17:48:53: 7000000 INFO @ Tue, 02 Aug 2022 17:48:57: 3000000 INFO @ Tue, 02 Aug 2022 17:49:00: 8000000 INFO @ Tue, 02 Aug 2022 17:49:04: 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 17:49:07: 9000000 INFO @ Tue, 02 Aug 2022 17:49:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.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 17:49:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:49:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:49:10: 5000000 INFO @ Tue, 02 Aug 2022 17:49:14: 10000000 INFO @ Tue, 02 Aug 2022 17:49:15: 1000000 INFO @ Tue, 02 Aug 2022 17:49:16: 6000000 INFO @ Tue, 02 Aug 2022 17:49:20: 11000000 INFO @ Tue, 02 Aug 2022 17:49:21: 2000000 INFO @ Tue, 02 Aug 2022 17:49:22: 7000000 INFO @ Tue, 02 Aug 2022 17:49:27: 12000000 INFO @ Tue, 02 Aug 2022 17:49:27: 3000000 INFO @ Tue, 02 Aug 2022 17:49:29: 8000000 INFO @ Tue, 02 Aug 2022 17:49:34: 4000000 INFO @ Tue, 02 Aug 2022 17:49:34: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:49:34: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:49:34: #1 total tags in treatment: 12963063 INFO @ Tue, 02 Aug 2022 17:49:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:49:34: #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 17:49:34: #1 tags after filtering in treatment: 12963063 INFO @ Tue, 02 Aug 2022 17:49:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:49:34: #1 finished! INFO @ Tue, 02 Aug 2022 17:49:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:49:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:49:35: 9000000 INFO @ Tue, 02 Aug 2022 17:49:35: #2 number of paired peaks: 125 WARNING @ Tue, 02 Aug 2022 17:49:35: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 02 Aug 2022 17:49:35: start model_add_line... INFO @ Tue, 02 Aug 2022 17:49:35: start X-correlation... INFO @ Tue, 02 Aug 2022 17:49:35: end of X-cor INFO @ Tue, 02 Aug 2022 17:49:35: #2 finished! INFO @ Tue, 02 Aug 2022 17:49:35: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 17:49:35: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 17:49:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.05_model.r WARNING @ Tue, 02 Aug 2022 17:49:35: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:49:35: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 17:49:35: #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 17:49:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:49:40: 5000000 INFO @ Tue, 02 Aug 2022 17:49:41: 10000000 INFO @ Tue, 02 Aug 2022 17:49:46: 6000000 INFO @ Tue, 02 Aug 2022 17:49:47: 11000000 INFO @ Tue, 02 Aug 2022 17:49:53: 7000000 INFO @ Tue, 02 Aug 2022 17:49:54: 12000000 INFO @ Tue, 02 Aug 2022 17:49:59: 8000000 INFO @ Tue, 02 Aug 2022 17:50:00: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:50:00: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:50:00: #1 total tags in treatment: 12963063 INFO @ Tue, 02 Aug 2022 17:50:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:50:00: #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 17:50:00: #1 tags after filtering in treatment: 12963063 INFO @ Tue, 02 Aug 2022 17:50:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:50:00: #1 finished! INFO @ Tue, 02 Aug 2022 17:50:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:50:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:50:01: #2 number of paired peaks: 125 WARNING @ Tue, 02 Aug 2022 17:50:01: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 02 Aug 2022 17:50:01: start model_add_line... INFO @ Tue, 02 Aug 2022 17:50:01: start X-correlation... INFO @ Tue, 02 Aug 2022 17:50:01: end of X-cor INFO @ Tue, 02 Aug 2022 17:50:01: #2 finished! INFO @ Tue, 02 Aug 2022 17:50:01: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 17:50:01: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 17:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.10_model.r WARNING @ Tue, 02 Aug 2022 17:50:01: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:50:01: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 17:50:01: #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 17:50:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:50:05: 9000000 INFO @ Tue, 02 Aug 2022 17:50:11: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.05_summits.bed INFO @ Tue, 02 Aug 2022 17:50:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5614 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:50:17: 11000000 INFO @ Tue, 02 Aug 2022 17:50:23: 12000000 INFO @ Tue, 02 Aug 2022 17:50:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:50:29: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:50:29: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:50:29: #1 total tags in treatment: 12963063 INFO @ Tue, 02 Aug 2022 17:50:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:50:29: #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 17:50:29: #1 tags after filtering in treatment: 12963063 INFO @ Tue, 02 Aug 2022 17:50:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:50:29: #1 finished! INFO @ Tue, 02 Aug 2022 17:50:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:50:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:50:30: #2 number of paired peaks: 125 WARNING @ Tue, 02 Aug 2022 17:50:30: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 02 Aug 2022 17:50:30: start model_add_line... INFO @ Tue, 02 Aug 2022 17:50:30: start X-correlation... INFO @ Tue, 02 Aug 2022 17:50:30: end of X-cor INFO @ Tue, 02 Aug 2022 17:50:30: #2 finished! INFO @ Tue, 02 Aug 2022 17:50:30: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 17:50:30: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 17:50:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.20_model.r WARNING @ Tue, 02 Aug 2022 17:50:30: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:50:30: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 17:50:30: #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 17:50:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:50:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.10_summits.bed INFO @ Tue, 02 Aug 2022 17:50:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2321 records, 4 fields): 40 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:50:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:51:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:51:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:51:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369006/SRX15369006.20_summits.bed INFO @ Tue, 02 Aug 2022 17:51:08: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (668 records, 4 fields): 37 millis CompletedMACS2peakCalling