Job ID = 14167048 SRX = SRX8574279 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 56648339 spots for SRR12045600/SRR12045600.sra Written 56648339 spots for SRR12045600/SRR12045600.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167484 ("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: 00:22:41 56648339 reads; of these: 56648339 (100.00%) were unpaired; of these: 6160352 (10.87%) aligned 0 times 36657150 (64.71%) aligned exactly 1 time 13830837 (24.42%) aligned >1 times 89.13% overall alignment rate Time searching: 00:22:41 Overall time: 00:22:41 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 24 files... [bam_rmdupse_core] 13275690 / 50487987 = 0.2629 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 09:58:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.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 09:58:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:58:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:58:36: 1000000 INFO @ Fri, 10 Dec 2021 09:58:42: 2000000 INFO @ Fri, 10 Dec 2021 09:58:48: 3000000 INFO @ Fri, 10 Dec 2021 09:58:54: 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 09:59:00: 5000000 INFO @ Fri, 10 Dec 2021 09:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.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 09:59:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:59:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:59:06: 6000000 INFO @ Fri, 10 Dec 2021 09:59:07: 1000000 INFO @ Fri, 10 Dec 2021 09:59:13: 7000000 INFO @ Fri, 10 Dec 2021 09:59:13: 2000000 INFO @ Fri, 10 Dec 2021 09:59:20: 8000000 INFO @ Fri, 10 Dec 2021 09:59:20: 3000000 INFO @ Fri, 10 Dec 2021 09:59:26: 9000000 INFO @ Fri, 10 Dec 2021 09:59:26: 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 09:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.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 09:59:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:59:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:59:33: 10000000 INFO @ Fri, 10 Dec 2021 09:59:33: 5000000 INFO @ Fri, 10 Dec 2021 09:59:38: 1000000 INFO @ Fri, 10 Dec 2021 09:59:40: 11000000 INFO @ Fri, 10 Dec 2021 09:59:40: 6000000 INFO @ Fri, 10 Dec 2021 09:59:46: 2000000 INFO @ Fri, 10 Dec 2021 09:59:48: 12000000 INFO @ Fri, 10 Dec 2021 09:59:48: 7000000 INFO @ Fri, 10 Dec 2021 09:59:54: 3000000 INFO @ Fri, 10 Dec 2021 09:59:55: 13000000 INFO @ Fri, 10 Dec 2021 09:59:55: 8000000 INFO @ Fri, 10 Dec 2021 10:00:02: 4000000 INFO @ Fri, 10 Dec 2021 10:00:02: 14000000 INFO @ Fri, 10 Dec 2021 10:00:02: 9000000 INFO @ Fri, 10 Dec 2021 10:00:10: 10000000 INFO @ Fri, 10 Dec 2021 10:00:10: 15000000 INFO @ Fri, 10 Dec 2021 10:00:10: 5000000 INFO @ Fri, 10 Dec 2021 10:00:17: 11000000 INFO @ Fri, 10 Dec 2021 10:00:17: 16000000 INFO @ Fri, 10 Dec 2021 10:00:18: 6000000 INFO @ Fri, 10 Dec 2021 10:00:24: 12000000 INFO @ Fri, 10 Dec 2021 10:00:24: 17000000 INFO @ Fri, 10 Dec 2021 10:00:26: 7000000 INFO @ Fri, 10 Dec 2021 10:00:32: 13000000 INFO @ Fri, 10 Dec 2021 10:00:32: 18000000 INFO @ Fri, 10 Dec 2021 10:00:34: 8000000 INFO @ Fri, 10 Dec 2021 10:00:39: 19000000 INFO @ Fri, 10 Dec 2021 10:00:39: 14000000 INFO @ Fri, 10 Dec 2021 10:00:42: 9000000 INFO @ Fri, 10 Dec 2021 10:00:47: 20000000 INFO @ Fri, 10 Dec 2021 10:00:47: 15000000 INFO @ Fri, 10 Dec 2021 10:00:50: 10000000 INFO @ Fri, 10 Dec 2021 10:00:54: 21000000 INFO @ Fri, 10 Dec 2021 10:00:54: 16000000 INFO @ Fri, 10 Dec 2021 10:00:58: 11000000 INFO @ Fri, 10 Dec 2021 10:01:01: 22000000 INFO @ Fri, 10 Dec 2021 10:01:02: 17000000 INFO @ Fri, 10 Dec 2021 10:01:06: 12000000 INFO @ Fri, 10 Dec 2021 10:01:09: 23000000 INFO @ Fri, 10 Dec 2021 10:01:09: 18000000 INFO @ Fri, 10 Dec 2021 10:01:14: 13000000 INFO @ Fri, 10 Dec 2021 10:01:16: 24000000 INFO @ Fri, 10 Dec 2021 10:01:16: 19000000 INFO @ Fri, 10 Dec 2021 10:01:22: 14000000 INFO @ Fri, 10 Dec 2021 10:01:24: 25000000 INFO @ Fri, 10 Dec 2021 10:01:24: 20000000 INFO @ Fri, 10 Dec 2021 10:01:30: 15000000 INFO @ Fri, 10 Dec 2021 10:01:31: 26000000 INFO @ Fri, 10 Dec 2021 10:01:31: 21000000 INFO @ Fri, 10 Dec 2021 10:01:38: 22000000 INFO @ Fri, 10 Dec 2021 10:01:38: 27000000 INFO @ Fri, 10 Dec 2021 10:01:38: 16000000 INFO @ Fri, 10 Dec 2021 10:01:46: 23000000 INFO @ Fri, 10 Dec 2021 10:01:46: 28000000 INFO @ Fri, 10 Dec 2021 10:01:46: 17000000 INFO @ Fri, 10 Dec 2021 10:01:53: 24000000 INFO @ Fri, 10 Dec 2021 10:01:53: 29000000 INFO @ Fri, 10 Dec 2021 10:01:54: 18000000 INFO @ Fri, 10 Dec 2021 10:02:00: 25000000 INFO @ Fri, 10 Dec 2021 10:02:00: 30000000 INFO @ Fri, 10 Dec 2021 10:02:03: 19000000 INFO @ Fri, 10 Dec 2021 10:02:07: 26000000 INFO @ Fri, 10 Dec 2021 10:02:08: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:02:11: 20000000 INFO @ Fri, 10 Dec 2021 10:02:15: 27000000 INFO @ Fri, 10 Dec 2021 10:02:15: 32000000 INFO @ Fri, 10 Dec 2021 10:02:18: 21000000 INFO @ Fri, 10 Dec 2021 10:02:22: 28000000 INFO @ Fri, 10 Dec 2021 10:02:22: 33000000 INFO @ Fri, 10 Dec 2021 10:02:26: 22000000 INFO @ Fri, 10 Dec 2021 10:02:29: 29000000 INFO @ Fri, 10 Dec 2021 10:02:30: 34000000 INFO @ Fri, 10 Dec 2021 10:02:34: 23000000 INFO @ Fri, 10 Dec 2021 10:02:36: 30000000 INFO @ Fri, 10 Dec 2021 10:02:37: 35000000 INFO @ Fri, 10 Dec 2021 10:02:42: 24000000 INFO @ Fri, 10 Dec 2021 10:02:44: 31000000 INFO @ Fri, 10 Dec 2021 10:02:44: 36000000 INFO @ Fri, 10 Dec 2021 10:02:50: 25000000 INFO @ Fri, 10 Dec 2021 10:02:51: 32000000 INFO @ Fri, 10 Dec 2021 10:02:51: 37000000 INFO @ Fri, 10 Dec 2021 10:02:53: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:02:53: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:02:53: #1 total tags in treatment: 37212297 INFO @ Fri, 10 Dec 2021 10:02:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:02:53: #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 10:02:53: #1 tags after filtering in treatment: 37212297 INFO @ Fri, 10 Dec 2021 10:02:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:02:53: #1 finished! INFO @ Fri, 10 Dec 2021 10:02:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:02:55: #2 number of paired peaks: 147 WARNING @ Fri, 10 Dec 2021 10:02:55: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Fri, 10 Dec 2021 10:02:55: start model_add_line... INFO @ Fri, 10 Dec 2021 10:02:56: start X-correlation... INFO @ Fri, 10 Dec 2021 10:02:56: end of X-cor INFO @ Fri, 10 Dec 2021 10:02:56: #2 finished! INFO @ Fri, 10 Dec 2021 10:02:56: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 10:02:56: #2 alternative fragment length(s) may be 4,127 bps INFO @ Fri, 10 Dec 2021 10:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.05_model.r WARNING @ Fri, 10 Dec 2021 10:02:56: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:02:56: #2 You may need to consider one of the other alternative d(s): 4,127 WARNING @ Fri, 10 Dec 2021 10:02:56: #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 10:02:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:02:58: 33000000 INFO @ Fri, 10 Dec 2021 10:02:58: 26000000 INFO @ Fri, 10 Dec 2021 10:03:05: 34000000 INFO @ Fri, 10 Dec 2021 10:03:06: 27000000 INFO @ Fri, 10 Dec 2021 10:03:12: 35000000 INFO @ Fri, 10 Dec 2021 10:03:14: 28000000 INFO @ Fri, 10 Dec 2021 10:03:19: 36000000 INFO @ Fri, 10 Dec 2021 10:03:22: 29000000 INFO @ Fri, 10 Dec 2021 10:03:26: 37000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:03:27: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:03:27: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:03:27: #1 total tags in treatment: 37212297 INFO @ Fri, 10 Dec 2021 10:03:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:03:27: #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 10:03:28: #1 tags after filtering in treatment: 37212297 INFO @ Fri, 10 Dec 2021 10:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:03:28: #1 finished! INFO @ Fri, 10 Dec 2021 10:03:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:03:30: 30000000 INFO @ Fri, 10 Dec 2021 10:03:30: #2 number of paired peaks: 147 WARNING @ Fri, 10 Dec 2021 10:03:30: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Fri, 10 Dec 2021 10:03:30: start model_add_line... INFO @ Fri, 10 Dec 2021 10:03:30: start X-correlation... INFO @ Fri, 10 Dec 2021 10:03:30: end of X-cor INFO @ Fri, 10 Dec 2021 10:03:30: #2 finished! INFO @ Fri, 10 Dec 2021 10:03:30: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 10:03:30: #2 alternative fragment length(s) may be 4,127 bps INFO @ Fri, 10 Dec 2021 10:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.10_model.r WARNING @ Fri, 10 Dec 2021 10:03:30: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:03:30: #2 You may need to consider one of the other alternative d(s): 4,127 WARNING @ Fri, 10 Dec 2021 10:03:30: #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 10:03:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:03:37: 31000000 INFO @ Fri, 10 Dec 2021 10:03:44: 32000000 INFO @ Fri, 10 Dec 2021 10:03:52: 33000000 INFO @ Fri, 10 Dec 2021 10:03:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:03:59: 34000000 INFO @ Fri, 10 Dec 2021 10:04:06: 35000000 INFO @ Fri, 10 Dec 2021 10:04:13: 36000000 INFO @ Fri, 10 Dec 2021 10:04:20: 37000000 INFO @ Fri, 10 Dec 2021 10:04:22: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:04:22: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:04:22: #1 total tags in treatment: 37212297 INFO @ Fri, 10 Dec 2021 10:04:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:04:22: #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 10:04:22: #1 tags after filtering in treatment: 37212297 INFO @ Fri, 10 Dec 2021 10:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:04:22: #1 finished! INFO @ Fri, 10 Dec 2021 10:04:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:04:24: #2 number of paired peaks: 147 WARNING @ Fri, 10 Dec 2021 10:04:24: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Fri, 10 Dec 2021 10:04:24: start model_add_line... INFO @ Fri, 10 Dec 2021 10:04:25: start X-correlation... INFO @ Fri, 10 Dec 2021 10:04:25: end of X-cor INFO @ Fri, 10 Dec 2021 10:04:25: #2 finished! INFO @ Fri, 10 Dec 2021 10:04:25: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 10:04:25: #2 alternative fragment length(s) may be 4,127 bps INFO @ Fri, 10 Dec 2021 10:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.20_model.r WARNING @ Fri, 10 Dec 2021 10:04:25: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:04:25: #2 You may need to consider one of the other alternative d(s): 4,127 WARNING @ Fri, 10 Dec 2021 10:04:25: #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 10:04:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.05_summits.bed INFO @ Fri, 10 Dec 2021 10:04:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9711 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:04:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:05:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:05:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:05:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.10_summits.bed INFO @ Fri, 10 Dec 2021 10:05:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6736 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:05:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574279/SRX8574279.20_summits.bed INFO @ Fri, 10 Dec 2021 10:05:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3849 records, 4 fields): 5 millis CompletedMACS2peakCalling