Job ID = 16438115 SRX = SRX10031709 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 75858412 spots for SRR13634479/SRR13634479.sra Written 75858412 spots for SRR13634479/SRR13634479.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439139 ("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: 00:43:58 75858412 reads; of these: 75858412 (100.00%) were unpaired; of these: 29514349 (38.91%) aligned 0 times 29856614 (39.36%) aligned exactly 1 time 16487449 (21.73%) aligned >1 times 61.09% overall alignment rate Time searching: 00:43:58 Overall time: 00:43:58 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 20 files... [bam_rmdupse_core] 21362589 / 46344063 = 0.4610 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 14:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.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 14:38:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:38:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:38:58: 1000000 INFO @ Tue, 02 Aug 2022 14:39:03: 2000000 INFO @ Tue, 02 Aug 2022 14:39:08: 3000000 INFO @ Tue, 02 Aug 2022 14:39:14: 4000000 INFO @ Tue, 02 Aug 2022 14:39:20: 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 14:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.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 14:39:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:39:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:39:25: 6000000 INFO @ Tue, 02 Aug 2022 14:39:28: 1000000 INFO @ Tue, 02 Aug 2022 14:39:31: 7000000 INFO @ Tue, 02 Aug 2022 14:39:34: 2000000 INFO @ Tue, 02 Aug 2022 14:39:37: 8000000 INFO @ Tue, 02 Aug 2022 14:39:39: 3000000 INFO @ Tue, 02 Aug 2022 14:39:42: 9000000 INFO @ Tue, 02 Aug 2022 14:39:45: 4000000 INFO @ Tue, 02 Aug 2022 14:39:48: 10000000 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 14:39:50: 5000000 INFO @ Tue, 02 Aug 2022 14:39:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.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 14:39:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:39:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:39:54: 11000000 INFO @ Tue, 02 Aug 2022 14:39:56: 6000000 INFO @ Tue, 02 Aug 2022 14:39:58: 1000000 INFO @ Tue, 02 Aug 2022 14:40:00: 12000000 INFO @ Tue, 02 Aug 2022 14:40:01: 7000000 INFO @ Tue, 02 Aug 2022 14:40:04: 2000000 INFO @ Tue, 02 Aug 2022 14:40:05: 13000000 INFO @ Tue, 02 Aug 2022 14:40:07: 8000000 INFO @ Tue, 02 Aug 2022 14:40:11: 3000000 INFO @ Tue, 02 Aug 2022 14:40:11: 14000000 INFO @ Tue, 02 Aug 2022 14:40:12: 9000000 INFO @ Tue, 02 Aug 2022 14:40:17: 15000000 INFO @ Tue, 02 Aug 2022 14:40:17: 4000000 INFO @ Tue, 02 Aug 2022 14:40:18: 10000000 INFO @ Tue, 02 Aug 2022 14:40:23: 16000000 INFO @ Tue, 02 Aug 2022 14:40:23: 11000000 INFO @ Tue, 02 Aug 2022 14:40:23: 5000000 INFO @ Tue, 02 Aug 2022 14:40:29: 12000000 INFO @ Tue, 02 Aug 2022 14:40:29: 17000000 INFO @ Tue, 02 Aug 2022 14:40:30: 6000000 INFO @ Tue, 02 Aug 2022 14:40:34: 13000000 INFO @ Tue, 02 Aug 2022 14:40:35: 18000000 INFO @ Tue, 02 Aug 2022 14:40:36: 7000000 INFO @ Tue, 02 Aug 2022 14:40:40: 14000000 INFO @ Tue, 02 Aug 2022 14:40:41: 19000000 INFO @ Tue, 02 Aug 2022 14:40:43: 8000000 INFO @ Tue, 02 Aug 2022 14:40:46: 15000000 INFO @ Tue, 02 Aug 2022 14:40:47: 20000000 INFO @ Tue, 02 Aug 2022 14:40:49: 9000000 INFO @ Tue, 02 Aug 2022 14:40:51: 16000000 INFO @ Tue, 02 Aug 2022 14:40:53: 21000000 INFO @ Tue, 02 Aug 2022 14:40:56: 10000000 INFO @ Tue, 02 Aug 2022 14:40:57: 17000000 INFO @ Tue, 02 Aug 2022 14:40:59: 22000000 INFO @ Tue, 02 Aug 2022 14:41:02: 11000000 INFO @ Tue, 02 Aug 2022 14:41:02: 18000000 INFO @ Tue, 02 Aug 2022 14:41:05: 23000000 INFO @ Tue, 02 Aug 2022 14:41:08: 19000000 INFO @ Tue, 02 Aug 2022 14:41:08: 12000000 INFO @ Tue, 02 Aug 2022 14:41:11: 24000000 INFO @ Tue, 02 Aug 2022 14:41:13: 20000000 INFO @ Tue, 02 Aug 2022 14:41:14: 13000000 INFO @ Tue, 02 Aug 2022 14:41:17: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:41:17: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:41:17: #1 total tags in treatment: 24981474 INFO @ Tue, 02 Aug 2022 14:41:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:41:17: #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 14:41:18: #1 tags after filtering in treatment: 24981474 INFO @ Tue, 02 Aug 2022 14:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:41:18: #1 finished! INFO @ Tue, 02 Aug 2022 14:41:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:41:18: 21000000 INFO @ Tue, 02 Aug 2022 14:41:19: #2 number of paired peaks: 2371 INFO @ Tue, 02 Aug 2022 14:41:19: start model_add_line... INFO @ Tue, 02 Aug 2022 14:41:20: start X-correlation... INFO @ Tue, 02 Aug 2022 14:41:20: end of X-cor INFO @ Tue, 02 Aug 2022 14:41:20: #2 finished! INFO @ Tue, 02 Aug 2022 14:41:20: #2 predicted fragment length is 39 bps INFO @ Tue, 02 Aug 2022 14:41:20: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 02 Aug 2022 14:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.05_model.r WARNING @ Tue, 02 Aug 2022 14:41:20: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:41:20: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 02 Aug 2022 14:41:20: #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 14:41:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:41:20: 14000000 INFO @ Tue, 02 Aug 2022 14:41:24: 22000000 INFO @ Tue, 02 Aug 2022 14:41:27: 15000000 INFO @ Tue, 02 Aug 2022 14:41:29: 23000000 INFO @ Tue, 02 Aug 2022 14:41:33: 16000000 INFO @ Tue, 02 Aug 2022 14:41:35: 24000000 INFO @ Tue, 02 Aug 2022 14:41:39: 17000000 INFO @ Tue, 02 Aug 2022 14:41:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:41:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:41:40: #1 total tags in treatment: 24981474 INFO @ Tue, 02 Aug 2022 14:41:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:41:40: #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 14:41:41: #1 tags after filtering in treatment: 24981474 INFO @ Tue, 02 Aug 2022 14:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:41:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:41:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:41:42: #2 number of paired peaks: 2371 INFO @ Tue, 02 Aug 2022 14:41:42: start model_add_line... INFO @ Tue, 02 Aug 2022 14:41:43: start X-correlation... INFO @ Tue, 02 Aug 2022 14:41:43: end of X-cor INFO @ Tue, 02 Aug 2022 14:41:43: #2 finished! INFO @ Tue, 02 Aug 2022 14:41:43: #2 predicted fragment length is 39 bps INFO @ Tue, 02 Aug 2022 14:41:43: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 02 Aug 2022 14:41:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.10_model.r WARNING @ Tue, 02 Aug 2022 14:41:43: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:41:43: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 02 Aug 2022 14:41:43: #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 14:41:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:41:45: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:41:51: 19000000 INFO @ Tue, 02 Aug 2022 14:41:58: 20000000 INFO @ Tue, 02 Aug 2022 14:42:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:04: 21000000 INFO @ Tue, 02 Aug 2022 14:42:10: 22000000 INFO @ Tue, 02 Aug 2022 14:42:16: 23000000 INFO @ Tue, 02 Aug 2022 14:42:22: 24000000 INFO @ Tue, 02 Aug 2022 14:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.05_summits.bed INFO @ Tue, 02 Aug 2022 14:42:24: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (25669 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:42:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:29: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:42:29: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:42:29: #1 total tags in treatment: 24981474 INFO @ Tue, 02 Aug 2022 14:42:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:29: #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 14:42:29: #1 tags after filtering in treatment: 24981474 INFO @ Tue, 02 Aug 2022 14:42:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:29: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:31: #2 number of paired peaks: 2371 INFO @ Tue, 02 Aug 2022 14:42:31: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:31: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:31: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:31: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:31: #2 predicted fragment length is 39 bps INFO @ Tue, 02 Aug 2022 14:42:31: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 02 Aug 2022 14:42:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.20_model.r WARNING @ Tue, 02 Aug 2022 14:42:31: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:31: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 02 Aug 2022 14:42:31: #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 14:42:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:42:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.10_summits.bed INFO @ Tue, 02 Aug 2022 14:42:49: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (18631 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:43:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031709/SRX10031709.20_summits.bed INFO @ Tue, 02 Aug 2022 14:43:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10877 records, 4 fields): 16 millis CompletedMACS2peakCalling