Job ID = 16438108 SRX = SRX10031707 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26381193 spots for SRR13634477/SRR13634477.sra Written 26381193 spots for SRR13634477/SRR13634477.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438582 ("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: 00:16:16 26381193 reads; of these: 26381193 (100.00%) were unpaired; of these: 903042 (3.42%) aligned 0 times 18917192 (71.71%) aligned exactly 1 time 6560959 (24.87%) aligned >1 times 96.58% overall alignment rate Time searching: 00:16:16 Overall time: 00:16:16 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] 4112748 / 25478151 = 0.1614 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 14:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.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 14:05:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:05:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:05:17: 1000000 INFO @ Tue, 02 Aug 2022 14:05:27: 2000000 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 14:05:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.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 14:05:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:05:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:05:37: 3000000 INFO @ Tue, 02 Aug 2022 14:05:47: 1000000 INFO @ Tue, 02 Aug 2022 14:05:48: 4000000 INFO @ Tue, 02 Aug 2022 14:05:59: 5000000 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 14:06:02: 2000000 INFO @ Tue, 02 Aug 2022 14:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.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 14:06:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:06:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:06:10: 6000000 INFO @ Tue, 02 Aug 2022 14:06:16: 1000000 INFO @ Tue, 02 Aug 2022 14:06:17: 3000000 INFO @ Tue, 02 Aug 2022 14:06:21: 7000000 INFO @ Tue, 02 Aug 2022 14:06:30: 2000000 INFO @ Tue, 02 Aug 2022 14:06:32: 4000000 INFO @ Tue, 02 Aug 2022 14:06:33: 8000000 INFO @ Tue, 02 Aug 2022 14:06:44: 9000000 INFO @ Tue, 02 Aug 2022 14:06:45: 3000000 INFO @ Tue, 02 Aug 2022 14:06:47: 5000000 INFO @ Tue, 02 Aug 2022 14:06:54: 10000000 INFO @ Tue, 02 Aug 2022 14:06:58: 4000000 INFO @ Tue, 02 Aug 2022 14:07:01: 6000000 INFO @ Tue, 02 Aug 2022 14:07:05: 11000000 INFO @ Tue, 02 Aug 2022 14:07:12: 5000000 INFO @ Tue, 02 Aug 2022 14:07:16: 7000000 INFO @ Tue, 02 Aug 2022 14:07:16: 12000000 INFO @ Tue, 02 Aug 2022 14:07:26: 6000000 INFO @ Tue, 02 Aug 2022 14:07:28: 13000000 INFO @ Tue, 02 Aug 2022 14:07:31: 8000000 INFO @ Tue, 02 Aug 2022 14:07:39: 14000000 INFO @ Tue, 02 Aug 2022 14:07:40: 7000000 INFO @ Tue, 02 Aug 2022 14:07:45: 9000000 INFO @ Tue, 02 Aug 2022 14:07:51: 15000000 INFO @ Tue, 02 Aug 2022 14:07:53: 8000000 INFO @ Tue, 02 Aug 2022 14:08:00: 10000000 INFO @ Tue, 02 Aug 2022 14:08:03: 16000000 INFO @ Tue, 02 Aug 2022 14:08:08: 9000000 INFO @ Tue, 02 Aug 2022 14:08:14: 17000000 INFO @ Tue, 02 Aug 2022 14:08:15: 11000000 INFO @ Tue, 02 Aug 2022 14:08:21: 10000000 INFO @ Tue, 02 Aug 2022 14:08:25: 18000000 INFO @ Tue, 02 Aug 2022 14:08:29: 12000000 INFO @ Tue, 02 Aug 2022 14:08:34: 11000000 INFO @ Tue, 02 Aug 2022 14:08:36: 19000000 INFO @ Tue, 02 Aug 2022 14:08:44: 13000000 INFO @ Tue, 02 Aug 2022 14:08:47: 20000000 INFO @ Tue, 02 Aug 2022 14:08:48: 12000000 INFO @ Tue, 02 Aug 2022 14:08:58: 21000000 INFO @ Tue, 02 Aug 2022 14:09:00: 14000000 INFO @ Tue, 02 Aug 2022 14:09:01: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:09:01: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:09:01: #1 total tags in treatment: 21365403 INFO @ Tue, 02 Aug 2022 14:09:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:09:01: #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 14:09:02: 13000000 INFO @ Tue, 02 Aug 2022 14:09:02: #1 tags after filtering in treatment: 21365403 INFO @ Tue, 02 Aug 2022 14:09:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:09:02: #1 finished! INFO @ Tue, 02 Aug 2022 14:09:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:09:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:09:04: #2 number of paired peaks: 467 WARNING @ Tue, 02 Aug 2022 14:09:04: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Tue, 02 Aug 2022 14:09:04: start model_add_line... INFO @ Tue, 02 Aug 2022 14:09:04: start X-correlation... INFO @ Tue, 02 Aug 2022 14:09:04: end of X-cor INFO @ Tue, 02 Aug 2022 14:09:04: #2 finished! INFO @ Tue, 02 Aug 2022 14:09:04: #2 predicted fragment length is 130 bps INFO @ Tue, 02 Aug 2022 14:09:04: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 02 Aug 2022 14:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.05_model.r WARNING @ Tue, 02 Aug 2022 14:09:04: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:09:04: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Tue, 02 Aug 2022 14:09:04: #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 14:09:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:09:13: 15000000 INFO @ Tue, 02 Aug 2022 14:09:15: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:09:28: 16000000 INFO @ Tue, 02 Aug 2022 14:09:29: 15000000 INFO @ Tue, 02 Aug 2022 14:09:42: 17000000 INFO @ Tue, 02 Aug 2022 14:09:43: 16000000 INFO @ Tue, 02 Aug 2022 14:09:55: 18000000 INFO @ Tue, 02 Aug 2022 14:09:56: 17000000 INFO @ Tue, 02 Aug 2022 14:10:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:10:09: 19000000 INFO @ Tue, 02 Aug 2022 14:10:10: 18000000 INFO @ Tue, 02 Aug 2022 14:10:23: 20000000 INFO @ Tue, 02 Aug 2022 14:10:23: 19000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:10:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:10:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:10:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.05_summits.bed INFO @ Tue, 02 Aug 2022 14:10:34: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10127 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:10:36: 21000000 INFO @ Tue, 02 Aug 2022 14:10:36: 20000000 INFO @ Tue, 02 Aug 2022 14:10:41: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:10:41: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:10:41: #1 total tags in treatment: 21365403 INFO @ Tue, 02 Aug 2022 14:10:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:10:41: #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 14:10:41: #1 tags after filtering in treatment: 21365403 INFO @ Tue, 02 Aug 2022 14:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:10:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:10:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:10:43: #2 number of paired peaks: 467 WARNING @ Tue, 02 Aug 2022 14:10:43: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Tue, 02 Aug 2022 14:10:43: start model_add_line... INFO @ Tue, 02 Aug 2022 14:10:43: start X-correlation... INFO @ Tue, 02 Aug 2022 14:10:43: end of X-cor INFO @ Tue, 02 Aug 2022 14:10:43: #2 finished! INFO @ Tue, 02 Aug 2022 14:10:43: #2 predicted fragment length is 130 bps INFO @ Tue, 02 Aug 2022 14:10:43: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 02 Aug 2022 14:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.10_model.r WARNING @ Tue, 02 Aug 2022 14:10:43: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:10:43: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Tue, 02 Aug 2022 14:10:43: #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 14:10:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:10:50: 21000000 INFO @ Tue, 02 Aug 2022 14:10:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:10:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:10:55: #1 total tags in treatment: 21365403 INFO @ Tue, 02 Aug 2022 14:10:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:10:55: #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 14:10:55: #1 tags after filtering in treatment: 21365403 INFO @ Tue, 02 Aug 2022 14:10:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:10:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:10:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:10:57: #2 number of paired peaks: 467 WARNING @ Tue, 02 Aug 2022 14:10:57: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Tue, 02 Aug 2022 14:10:57: start model_add_line... INFO @ Tue, 02 Aug 2022 14:10:57: start X-correlation... INFO @ Tue, 02 Aug 2022 14:10:57: end of X-cor INFO @ Tue, 02 Aug 2022 14:10:57: #2 finished! INFO @ Tue, 02 Aug 2022 14:10:57: #2 predicted fragment length is 130 bps INFO @ Tue, 02 Aug 2022 14:10:57: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 02 Aug 2022 14:10:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.20_model.r WARNING @ Tue, 02 Aug 2022 14:10:57: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:10:57: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Tue, 02 Aug 2022 14:10:57: #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 14:10:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:11:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:11:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:12:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:12:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:12:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.10_summits.bed INFO @ Tue, 02 Aug 2022 14:12:16: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7418 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:12:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:12:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:12:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031707/SRX10031707.20_summits.bed INFO @ Tue, 02 Aug 2022 14:12:30: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4402 records, 4 fields): 52 millis CompletedMACS2peakCalling