Job ID = 14171969 SRX = SRX9427717 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23824592 spots for SRR12975524/SRR12975524.sra Written 23824592 spots for SRR12975524/SRR12975524.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172483 ("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: 00:13:28 23824592 reads; of these: 23824592 (100.00%) were unpaired; of these: 393949 (1.65%) aligned 0 times 4588160 (19.26%) aligned exactly 1 time 18842483 (79.09%) aligned >1 times 98.35% overall alignment rate Time searching: 00:13:28 Overall time: 00:13:28 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] 7963571 / 23430643 = 0.3399 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.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 @ Sat, 11 Dec 2021 13:54:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:54:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:54:52: 1000000 INFO @ Sat, 11 Dec 2021 13:54:57: 2000000 INFO @ Sat, 11 Dec 2021 13:55:02: 3000000 INFO @ Sat, 11 Dec 2021 13:55:06: 4000000 INFO @ Sat, 11 Dec 2021 13:55:11: 5000000 INFO @ Sat, 11 Dec 2021 13:55:16: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.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 @ Sat, 11 Dec 2021 13:55:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:55:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:55:20: 7000000 INFO @ Sat, 11 Dec 2021 13:55:22: 1000000 INFO @ Sat, 11 Dec 2021 13:55:25: 8000000 INFO @ Sat, 11 Dec 2021 13:55:27: 2000000 INFO @ Sat, 11 Dec 2021 13:55:30: 9000000 INFO @ Sat, 11 Dec 2021 13:55:31: 3000000 INFO @ Sat, 11 Dec 2021 13:55:34: 10000000 INFO @ Sat, 11 Dec 2021 13:55:36: 4000000 INFO @ Sat, 11 Dec 2021 13:55:39: 11000000 INFO @ Sat, 11 Dec 2021 13:55:41: 5000000 INFO @ Sat, 11 Dec 2021 13:55:44: 12000000 INFO @ Sat, 11 Dec 2021 13:55:45: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.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 @ Sat, 11 Dec 2021 13:55:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:55:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:55:49: 13000000 INFO @ Sat, 11 Dec 2021 13:55:50: 7000000 INFO @ Sat, 11 Dec 2021 13:55:53: 1000000 INFO @ Sat, 11 Dec 2021 13:55:53: 14000000 INFO @ Sat, 11 Dec 2021 13:55:55: 8000000 INFO @ Sat, 11 Dec 2021 13:55:58: 2000000 INFO @ Sat, 11 Dec 2021 13:55:58: 15000000 INFO @ Sat, 11 Dec 2021 13:56:00: 9000000 INFO @ Sat, 11 Dec 2021 13:56:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:56:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:56:01: #1 total tags in treatment: 15467072 INFO @ Sat, 11 Dec 2021 13:56:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:56:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:56:01: #1 tags after filtering in treatment: 15467072 INFO @ Sat, 11 Dec 2021 13:56:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:56:01: #1 finished! INFO @ Sat, 11 Dec 2021 13:56:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:56:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:56:02: #2 number of paired peaks: 7587 INFO @ Sat, 11 Dec 2021 13:56:02: start model_add_line... INFO @ Sat, 11 Dec 2021 13:56:03: 3000000 INFO @ Sat, 11 Dec 2021 13:56:03: start X-correlation... INFO @ Sat, 11 Dec 2021 13:56:03: end of X-cor INFO @ Sat, 11 Dec 2021 13:56:03: #2 finished! INFO @ Sat, 11 Dec 2021 13:56:03: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:56:03: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 13:56:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.05_model.r WARNING @ Sat, 11 Dec 2021 13:56:03: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:56:03: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 13:56:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:56:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:56:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:56:04: 10000000 INFO @ Sat, 11 Dec 2021 13:56:07: 4000000 INFO @ Sat, 11 Dec 2021 13:56:09: 11000000 INFO @ Sat, 11 Dec 2021 13:56:12: 5000000 INFO @ Sat, 11 Dec 2021 13:56:14: 12000000 INFO @ Sat, 11 Dec 2021 13:56:17: 6000000 INFO @ Sat, 11 Dec 2021 13:56:18: 13000000 INFO @ Sat, 11 Dec 2021 13:56:22: 7000000 INFO @ Sat, 11 Dec 2021 13:56:23: 14000000 INFO @ Sat, 11 Dec 2021 13:56:27: 8000000 INFO @ Sat, 11 Dec 2021 13:56:28: 15000000 INFO @ Sat, 11 Dec 2021 13:56:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:56:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:56:30: #1 total tags in treatment: 15467072 INFO @ Sat, 11 Dec 2021 13:56:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:56:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:56:30: #1 tags after filtering in treatment: 15467072 INFO @ Sat, 11 Dec 2021 13:56:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:56:30: #1 finished! INFO @ Sat, 11 Dec 2021 13:56:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:56:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:56:31: 9000000 INFO @ Sat, 11 Dec 2021 13:56:32: #2 number of paired peaks: 7587 INFO @ Sat, 11 Dec 2021 13:56:32: start model_add_line... INFO @ Sat, 11 Dec 2021 13:56:32: start X-correlation... INFO @ Sat, 11 Dec 2021 13:56:32: end of X-cor INFO @ Sat, 11 Dec 2021 13:56:32: #2 finished! INFO @ Sat, 11 Dec 2021 13:56:32: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:56:32: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 13:56:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.10_model.r WARNING @ Sat, 11 Dec 2021 13:56:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:56:32: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 13:56:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:56:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:56:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:56:36: 10000000 INFO @ Sat, 11 Dec 2021 13:56:41: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:56:45: 12000000 INFO @ Sat, 11 Dec 2021 13:56:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:56:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:56:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.05_summits.bed INFO @ Sat, 11 Dec 2021 13:56:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (17649 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:56:50: 13000000 INFO @ Sat, 11 Dec 2021 13:56:54: 14000000 INFO @ Sat, 11 Dec 2021 13:56:59: 15000000 INFO @ Sat, 11 Dec 2021 13:56:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:57:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:57:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:57:01: #1 total tags in treatment: 15467072 INFO @ Sat, 11 Dec 2021 13:57:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:57:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:57:02: #1 tags after filtering in treatment: 15467072 INFO @ Sat, 11 Dec 2021 13:57:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:57:02: #1 finished! INFO @ Sat, 11 Dec 2021 13:57:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:57:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:57:03: #2 number of paired peaks: 7587 INFO @ Sat, 11 Dec 2021 13:57:03: start model_add_line... INFO @ Sat, 11 Dec 2021 13:57:03: start X-correlation... INFO @ Sat, 11 Dec 2021 13:57:03: end of X-cor INFO @ Sat, 11 Dec 2021 13:57:03: #2 finished! INFO @ Sat, 11 Dec 2021 13:57:03: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 13:57:03: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 13:57:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.20_model.r WARNING @ Sat, 11 Dec 2021 13:57:03: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:57:03: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 13:57:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:57:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:57:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:57:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:57:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:57:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.10_summits.bed INFO @ Sat, 11 Dec 2021 13:57:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11926 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:57:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:57:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:57:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:57:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427717/SRX9427717.20_summits.bed INFO @ Sat, 11 Dec 2021 13:57:48: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (5007 records, 4 fields): 6 millis CompletedMACS2peakCalling