Job ID = 14168465 SRX = SRX9730750 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27590513 spots for SRR13301828/SRR13301828.sra Written 27590513 spots for SRR13301828/SRR13301828.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169616 ("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: 00:10:04 27590513 reads; of these: 27590513 (100.00%) were unpaired; of these: 1081262 (3.92%) aligned 0 times 20155270 (73.05%) aligned exactly 1 time 6353981 (23.03%) aligned >1 times 96.08% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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] 4601484 / 26509251 = 0.1736 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 @ Fri, 10 Dec 2021 18:50:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.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 @ Fri, 10 Dec 2021 18:50:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:50:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:50:31: 1000000 INFO @ Fri, 10 Dec 2021 18:50:37: 2000000 INFO @ Fri, 10 Dec 2021 18:50:42: 3000000 INFO @ Fri, 10 Dec 2021 18:50:48: 4000000 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 @ Fri, 10 Dec 2021 18:50:54: 5000000 INFO @ Fri, 10 Dec 2021 18:50:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.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 @ Fri, 10 Dec 2021 18:50:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:50:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:51:00: 6000000 INFO @ Fri, 10 Dec 2021 18:51:02: 1000000 INFO @ Fri, 10 Dec 2021 18:51:06: 7000000 INFO @ Fri, 10 Dec 2021 18:51:08: 2000000 INFO @ Fri, 10 Dec 2021 18:51:13: 8000000 INFO @ Fri, 10 Dec 2021 18:51:14: 3000000 INFO @ Fri, 10 Dec 2021 18:51:19: 9000000 INFO @ Fri, 10 Dec 2021 18:51:21: 4000000 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 @ Fri, 10 Dec 2021 18:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.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 @ Fri, 10 Dec 2021 18:51:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:51:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:51:26: 10000000 INFO @ Fri, 10 Dec 2021 18:51:27: 5000000 INFO @ Fri, 10 Dec 2021 18:51:33: 11000000 INFO @ Fri, 10 Dec 2021 18:51:33: 1000000 INFO @ Fri, 10 Dec 2021 18:51:34: 6000000 INFO @ Fri, 10 Dec 2021 18:51:40: 12000000 INFO @ Fri, 10 Dec 2021 18:51:41: 2000000 INFO @ Fri, 10 Dec 2021 18:51:41: 7000000 INFO @ Fri, 10 Dec 2021 18:51:47: 13000000 INFO @ Fri, 10 Dec 2021 18:51:49: 8000000 INFO @ Fri, 10 Dec 2021 18:51:49: 3000000 INFO @ Fri, 10 Dec 2021 18:51:54: 14000000 INFO @ Fri, 10 Dec 2021 18:51:56: 9000000 INFO @ Fri, 10 Dec 2021 18:51:58: 4000000 INFO @ Fri, 10 Dec 2021 18:52:01: 15000000 INFO @ Fri, 10 Dec 2021 18:52:03: 10000000 INFO @ Fri, 10 Dec 2021 18:52:06: 5000000 INFO @ Fri, 10 Dec 2021 18:52:08: 16000000 INFO @ Fri, 10 Dec 2021 18:52:10: 11000000 INFO @ Fri, 10 Dec 2021 18:52:14: 6000000 INFO @ Fri, 10 Dec 2021 18:52:15: 17000000 INFO @ Fri, 10 Dec 2021 18:52:17: 12000000 INFO @ Fri, 10 Dec 2021 18:52:22: 18000000 INFO @ Fri, 10 Dec 2021 18:52:22: 7000000 INFO @ Fri, 10 Dec 2021 18:52:24: 13000000 INFO @ Fri, 10 Dec 2021 18:52:29: 19000000 INFO @ Fri, 10 Dec 2021 18:52:30: 8000000 INFO @ Fri, 10 Dec 2021 18:52:31: 14000000 INFO @ Fri, 10 Dec 2021 18:52:36: 20000000 INFO @ Fri, 10 Dec 2021 18:52:38: 15000000 INFO @ Fri, 10 Dec 2021 18:52:38: 9000000 INFO @ Fri, 10 Dec 2021 18:52:43: 21000000 INFO @ Fri, 10 Dec 2021 18:52:45: 16000000 INFO @ Fri, 10 Dec 2021 18:52:47: 10000000 INFO @ Fri, 10 Dec 2021 18:52:49: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:52:49: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:52:49: #1 total tags in treatment: 21907767 INFO @ Fri, 10 Dec 2021 18:52:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:52:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:52:49: #1 tags after filtering in treatment: 21907767 INFO @ Fri, 10 Dec 2021 18:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 18:52:49: #1 finished! INFO @ Fri, 10 Dec 2021 18:52:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:52:51: #2 number of paired peaks: 1467 INFO @ Fri, 10 Dec 2021 18:52:51: start model_add_line... INFO @ Fri, 10 Dec 2021 18:52:51: start X-correlation... INFO @ Fri, 10 Dec 2021 18:52:51: end of X-cor INFO @ Fri, 10 Dec 2021 18:52:51: #2 finished! INFO @ Fri, 10 Dec 2021 18:52:51: #2 predicted fragment length is 78 bps INFO @ Fri, 10 Dec 2021 18:52:51: #2 alternative fragment length(s) may be 1,78 bps INFO @ Fri, 10 Dec 2021 18:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.05_model.r WARNING @ Fri, 10 Dec 2021 18:52:51: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:52:51: #2 You may need to consider one of the other alternative d(s): 1,78 WARNING @ Fri, 10 Dec 2021 18:52:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 18:52:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:52:52: 17000000 INFO @ Fri, 10 Dec 2021 18:52:55: 11000000 INFO @ Fri, 10 Dec 2021 18:52:59: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:53:03: 12000000 INFO @ Fri, 10 Dec 2021 18:53:06: 19000000 INFO @ Fri, 10 Dec 2021 18:53:11: 13000000 INFO @ Fri, 10 Dec 2021 18:53:13: 20000000 INFO @ Fri, 10 Dec 2021 18:53:19: 14000000 INFO @ Fri, 10 Dec 2021 18:53:20: 21000000 INFO @ Fri, 10 Dec 2021 18:53:27: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:53:27: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:53:27: #1 total tags in treatment: 21907767 INFO @ Fri, 10 Dec 2021 18:53:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:53:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:53:27: #1 tags after filtering in treatment: 21907767 INFO @ Fri, 10 Dec 2021 18:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 18:53:27: #1 finished! INFO @ Fri, 10 Dec 2021 18:53:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:53:27: 15000000 INFO @ Fri, 10 Dec 2021 18:53:28: #2 number of paired peaks: 1467 INFO @ Fri, 10 Dec 2021 18:53:28: start model_add_line... INFO @ Fri, 10 Dec 2021 18:53:29: start X-correlation... INFO @ Fri, 10 Dec 2021 18:53:29: end of X-cor INFO @ Fri, 10 Dec 2021 18:53:29: #2 finished! INFO @ Fri, 10 Dec 2021 18:53:29: #2 predicted fragment length is 78 bps INFO @ Fri, 10 Dec 2021 18:53:29: #2 alternative fragment length(s) may be 1,78 bps INFO @ Fri, 10 Dec 2021 18:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.10_model.r WARNING @ Fri, 10 Dec 2021 18:53:29: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:53:29: #2 You may need to consider one of the other alternative d(s): 1,78 WARNING @ Fri, 10 Dec 2021 18:53:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 18:53:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:53:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:53:35: 16000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:53:42: 17000000 INFO @ Fri, 10 Dec 2021 18:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:53:49: 18000000 INFO @ Fri, 10 Dec 2021 18:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.05_summits.bed INFO @ Fri, 10 Dec 2021 18:53:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3810 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:53:57: 19000000 INFO @ Fri, 10 Dec 2021 18:54:04: 20000000 INFO @ Fri, 10 Dec 2021 18:54:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:54:11: 21000000 INFO @ Fri, 10 Dec 2021 18:54:18: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:54:18: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:54:18: #1 total tags in treatment: 21907767 INFO @ Fri, 10 Dec 2021 18:54:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:54:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:54:18: #1 tags after filtering in treatment: 21907767 INFO @ Fri, 10 Dec 2021 18:54:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 18:54:18: #1 finished! INFO @ Fri, 10 Dec 2021 18:54:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:54:20: #2 number of paired peaks: 1467 INFO @ Fri, 10 Dec 2021 18:54:20: start model_add_line... INFO @ Fri, 10 Dec 2021 18:54:20: start X-correlation... INFO @ Fri, 10 Dec 2021 18:54:20: end of X-cor INFO @ Fri, 10 Dec 2021 18:54:20: #2 finished! INFO @ Fri, 10 Dec 2021 18:54:20: #2 predicted fragment length is 78 bps INFO @ Fri, 10 Dec 2021 18:54:20: #2 alternative fragment length(s) may be 1,78 bps INFO @ Fri, 10 Dec 2021 18:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.20_model.r WARNING @ Fri, 10 Dec 2021 18:54:20: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:54:20: #2 You may need to consider one of the other alternative d(s): 1,78 WARNING @ Fri, 10 Dec 2021 18:54:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 18:54:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.10_summits.bed INFO @ Fri, 10 Dec 2021 18:54:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2138 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:55:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9730750/SRX9730750.20_summits.bed INFO @ Fri, 10 Dec 2021 18:55:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1168 records, 4 fields): 2 millis CompletedMACS2peakCalling