Job ID = 16438687 SRX = SRX15206501 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:03:01 prefetch.2.10.7: 1) Downloading 'SRR19139291'... 2022-08-02T05:03:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:03:20 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:03:20 prefetch.2.10.7: 'SRR19139291' is valid 2022-08-02T05:03:20 prefetch.2.10.7: 1) 'SRR19139291' was downloaded successfully 2022-08-02T05:03:20 prefetch.2.10.7: 'SRR19139291' has 0 unresolved dependencies Read 10328581 spots for SRR19139291/SRR19139291.sra Written 10328581 spots for SRR19139291/SRR19139291.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438927 ("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: 00:04:06 10328581 reads; of these: 10328581 (100.00%) were unpaired; of these: 248091 (2.40%) aligned 0 times 8375506 (81.09%) aligned exactly 1 time 1704984 (16.51%) aligned >1 times 97.60% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 463956 / 10080490 = 0.0460 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 14:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.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 14:12:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:12:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:12:11: 1000000 INFO @ Tue, 02 Aug 2022 14:12:18: 2000000 INFO @ Tue, 02 Aug 2022 14:12:26: 3000000 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 14:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.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 14:12:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:12:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:12:34: 4000000 INFO @ Tue, 02 Aug 2022 14:12:39: 1000000 INFO @ Tue, 02 Aug 2022 14:12:42: 5000000 INFO @ Tue, 02 Aug 2022 14:12:47: 2000000 INFO @ Tue, 02 Aug 2022 14:12:50: 6000000 INFO @ Tue, 02 Aug 2022 14:12:56: 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 14:12:59: 7000000 INFO @ Tue, 02 Aug 2022 14:13:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.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 14:13:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:13:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:13:04: 4000000 INFO @ Tue, 02 Aug 2022 14:13:08: 1000000 INFO @ Tue, 02 Aug 2022 14:13:08: 8000000 INFO @ Tue, 02 Aug 2022 14:13:13: 5000000 INFO @ Tue, 02 Aug 2022 14:13:15: 2000000 INFO @ Tue, 02 Aug 2022 14:13:17: 9000000 INFO @ Tue, 02 Aug 2022 14:13:22: 3000000 INFO @ Tue, 02 Aug 2022 14:13:22: 6000000 INFO @ Tue, 02 Aug 2022 14:13:23: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:13:23: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:13:23: #1 total tags in treatment: 9616534 INFO @ Tue, 02 Aug 2022 14:13:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:13:23: #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 14:13:23: #1 tags after filtering in treatment: 9616534 INFO @ Tue, 02 Aug 2022 14:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:13:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:13:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:13:23: #2 number of paired peaks: 126 WARNING @ Tue, 02 Aug 2022 14:13:23: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 02 Aug 2022 14:13:23: start model_add_line... INFO @ Tue, 02 Aug 2022 14:13:23: start X-correlation... INFO @ Tue, 02 Aug 2022 14:13:24: end of X-cor INFO @ Tue, 02 Aug 2022 14:13:24: #2 finished! INFO @ Tue, 02 Aug 2022 14:13:24: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:13:24: #2 alternative fragment length(s) may be 4,81,200,220 bps INFO @ Tue, 02 Aug 2022 14:13:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.05_model.r WARNING @ Tue, 02 Aug 2022 14:13:24: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:13:24: #2 You may need to consider one of the other alternative d(s): 4,81,200,220 WARNING @ Tue, 02 Aug 2022 14:13:24: #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 14:13:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:13:28: 4000000 INFO @ Tue, 02 Aug 2022 14:13:30: 7000000 INFO @ Tue, 02 Aug 2022 14:13:35: 5000000 INFO @ Tue, 02 Aug 2022 14:13:38: 8000000 INFO @ Tue, 02 Aug 2022 14:13:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:13:42: 6000000 INFO @ Tue, 02 Aug 2022 14:13:47: 9000000 INFO @ Tue, 02 Aug 2022 14:13:49: 7000000 INFO @ Tue, 02 Aug 2022 14:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.05_summits.bed INFO @ Tue, 02 Aug 2022 14:13:51: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:13:52: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:13:52: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:13:52: #1 total tags in treatment: 9616534 INFO @ Tue, 02 Aug 2022 14:13:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:13:52: #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 14:13:52: #1 tags after filtering in treatment: 9616534 INFO @ Tue, 02 Aug 2022 14:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:13:52: #1 finished! INFO @ Tue, 02 Aug 2022 14:13:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:13:52: #2 number of paired peaks: 126 WARNING @ Tue, 02 Aug 2022 14:13:52: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 02 Aug 2022 14:13:52: start model_add_line... INFO @ Tue, 02 Aug 2022 14:13:52: start X-correlation... INFO @ Tue, 02 Aug 2022 14:13:52: end of X-cor INFO @ Tue, 02 Aug 2022 14:13:52: #2 finished! INFO @ Tue, 02 Aug 2022 14:13:52: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:13:52: #2 alternative fragment length(s) may be 4,81,200,220 bps INFO @ Tue, 02 Aug 2022 14:13:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.10_model.r WARNING @ Tue, 02 Aug 2022 14:13:52: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:13:52: #2 You may need to consider one of the other alternative d(s): 4,81,200,220 WARNING @ Tue, 02 Aug 2022 14:13:52: #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 14:13:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:13:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:13:55: 8000000 INFO @ Tue, 02 Aug 2022 14:14:02: 9000000 INFO @ Tue, 02 Aug 2022 14:14:06: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:14:06: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:14:06: #1 total tags in treatment: 9616534 INFO @ Tue, 02 Aug 2022 14:14:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:14:06: #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 14:14:06: #1 tags after filtering in treatment: 9616534 INFO @ Tue, 02 Aug 2022 14:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:14:06: #1 finished! INFO @ Tue, 02 Aug 2022 14:14:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:14:07: #2 number of paired peaks: 126 WARNING @ Tue, 02 Aug 2022 14:14:07: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 02 Aug 2022 14:14:07: start model_add_line... INFO @ Tue, 02 Aug 2022 14:14:07: start X-correlation... INFO @ Tue, 02 Aug 2022 14:14:07: end of X-cor INFO @ Tue, 02 Aug 2022 14:14:07: #2 finished! INFO @ Tue, 02 Aug 2022 14:14:07: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:14:07: #2 alternative fragment length(s) may be 4,81,200,220 bps INFO @ Tue, 02 Aug 2022 14:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.20_model.r WARNING @ Tue, 02 Aug 2022 14:14:07: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:14:07: #2 You may need to consider one of the other alternative d(s): 4,81,200,220 WARNING @ Tue, 02 Aug 2022 14:14:07: #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 14:14:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:14:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:14:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:14:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:14:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:14:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.10_summits.bed INFO @ Tue, 02 Aug 2022 14:14:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (78 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:14:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206501/SRX15206501.20_summits.bed INFO @ Tue, 02 Aug 2022 14:14:33: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (38 records, 4 fields): 45 millis CompletedMACS2peakCalling BigWig に変換しました。