Job ID = 14170629 SRX = SRX9434465 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 36385042 spots for SRR12982863/SRR12982863.sra Written 36385042 spots for SRR12982863/SRR12982863.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171070 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:50 36385042 reads; of these: 36385042 (100.00%) were unpaired; of these: 780794 (2.15%) aligned 0 times 24402989 (67.07%) aligned exactly 1 time 11201259 (30.79%) aligned >1 times 97.85% overall alignment rate Time searching: 00:11:51 Overall time: 00:11:51 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 16 files... [bam_rmdupse_core] 7506040 / 35604248 = 0.2108 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 07:55:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.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 07:55:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:55:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:55:42: 1000000 INFO @ Sat, 11 Dec 2021 07:55:47: 2000000 INFO @ Sat, 11 Dec 2021 07:55:52: 3000000 INFO @ Sat, 11 Dec 2021 07:55:56: 4000000 INFO @ Sat, 11 Dec 2021 07:56:01: 5000000 INFO @ Sat, 11 Dec 2021 07:56:05: 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 07:56:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.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 07:56:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:56:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:56:10: 7000000 INFO @ Sat, 11 Dec 2021 07:56:13: 1000000 INFO @ Sat, 11 Dec 2021 07:56:15: 8000000 INFO @ Sat, 11 Dec 2021 07:56:19: 2000000 INFO @ Sat, 11 Dec 2021 07:56:20: 9000000 INFO @ Sat, 11 Dec 2021 07:56:25: 3000000 INFO @ Sat, 11 Dec 2021 07:56:25: 10000000 INFO @ Sat, 11 Dec 2021 07:56:30: 11000000 INFO @ Sat, 11 Dec 2021 07:56:31: 4000000 INFO @ Sat, 11 Dec 2021 07:56:35: 12000000 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 07:56:37: 5000000 INFO @ Sat, 11 Dec 2021 07:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.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 07:56:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:56:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:56:40: 13000000 INFO @ Sat, 11 Dec 2021 07:56:42: 6000000 INFO @ Sat, 11 Dec 2021 07:56:43: 1000000 INFO @ Sat, 11 Dec 2021 07:56:45: 14000000 INFO @ Sat, 11 Dec 2021 07:56:48: 2000000 INFO @ Sat, 11 Dec 2021 07:56:48: 7000000 INFO @ Sat, 11 Dec 2021 07:56:50: 15000000 INFO @ Sat, 11 Dec 2021 07:56:53: 3000000 INFO @ Sat, 11 Dec 2021 07:56:54: 8000000 INFO @ Sat, 11 Dec 2021 07:56:55: 16000000 INFO @ Sat, 11 Dec 2021 07:56:58: 4000000 INFO @ Sat, 11 Dec 2021 07:57:00: 9000000 INFO @ Sat, 11 Dec 2021 07:57:00: 17000000 INFO @ Sat, 11 Dec 2021 07:57:03: 5000000 INFO @ Sat, 11 Dec 2021 07:57:05: 18000000 INFO @ Sat, 11 Dec 2021 07:57:05: 10000000 INFO @ Sat, 11 Dec 2021 07:57:08: 6000000 INFO @ Sat, 11 Dec 2021 07:57:10: 19000000 INFO @ Sat, 11 Dec 2021 07:57:11: 11000000 INFO @ Sat, 11 Dec 2021 07:57:13: 7000000 INFO @ Sat, 11 Dec 2021 07:57:15: 20000000 INFO @ Sat, 11 Dec 2021 07:57:17: 12000000 INFO @ Sat, 11 Dec 2021 07:57:18: 8000000 INFO @ Sat, 11 Dec 2021 07:57:20: 21000000 INFO @ Sat, 11 Dec 2021 07:57:23: 13000000 INFO @ Sat, 11 Dec 2021 07:57:23: 9000000 INFO @ Sat, 11 Dec 2021 07:57:25: 22000000 INFO @ Sat, 11 Dec 2021 07:57:28: 10000000 INFO @ Sat, 11 Dec 2021 07:57:29: 14000000 INFO @ Sat, 11 Dec 2021 07:57:30: 23000000 INFO @ Sat, 11 Dec 2021 07:57:33: 11000000 INFO @ Sat, 11 Dec 2021 07:57:34: 15000000 INFO @ Sat, 11 Dec 2021 07:57:35: 24000000 INFO @ Sat, 11 Dec 2021 07:57:38: 12000000 INFO @ Sat, 11 Dec 2021 07:57:40: 16000000 INFO @ Sat, 11 Dec 2021 07:57:40: 25000000 INFO @ Sat, 11 Dec 2021 07:57:43: 13000000 INFO @ Sat, 11 Dec 2021 07:57:45: 26000000 INFO @ Sat, 11 Dec 2021 07:57:46: 17000000 INFO @ Sat, 11 Dec 2021 07:57:48: 14000000 INFO @ Sat, 11 Dec 2021 07:57:50: 27000000 INFO @ Sat, 11 Dec 2021 07:57:52: 18000000 INFO @ Sat, 11 Dec 2021 07:57:53: 15000000 INFO @ Sat, 11 Dec 2021 07:57:55: 28000000 INFO @ Sat, 11 Dec 2021 07:57:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:57:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:57:56: #1 total tags in treatment: 28098208 INFO @ Sat, 11 Dec 2021 07:57:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:57:56: #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 07:57:57: #1 tags after filtering in treatment: 28098208 INFO @ Sat, 11 Dec 2021 07:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:57:57: #1 finished! INFO @ Sat, 11 Dec 2021 07:57:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:57:58: 19000000 INFO @ Sat, 11 Dec 2021 07:57:58: 16000000 INFO @ Sat, 11 Dec 2021 07:57:58: #2 number of paired peaks: 142 WARNING @ Sat, 11 Dec 2021 07:57:58: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sat, 11 Dec 2021 07:57:58: start model_add_line... INFO @ Sat, 11 Dec 2021 07:57:58: start X-correlation... INFO @ Sat, 11 Dec 2021 07:57:58: end of X-cor INFO @ Sat, 11 Dec 2021 07:57:58: #2 finished! INFO @ Sat, 11 Dec 2021 07:57:58: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 07:57:58: #2 alternative fragment length(s) may be 1,43,455,536,544 bps INFO @ Sat, 11 Dec 2021 07:57:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.05_model.r WARNING @ Sat, 11 Dec 2021 07:57:58: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:57:58: #2 You may need to consider one of the other alternative d(s): 1,43,455,536,544 WARNING @ Sat, 11 Dec 2021 07:57:58: #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 07:57:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:57:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:58:03: 20000000 INFO @ Sat, 11 Dec 2021 07:58:03: 17000000 INFO @ Sat, 11 Dec 2021 07:58:08: 18000000 INFO @ Sat, 11 Dec 2021 07:58:09: 21000000 INFO @ Sat, 11 Dec 2021 07:58:13: 19000000 INFO @ Sat, 11 Dec 2021 07:58:14: 22000000 INFO @ Sat, 11 Dec 2021 07:58:18: 20000000 INFO @ Sat, 11 Dec 2021 07:58:20: 23000000 INFO @ Sat, 11 Dec 2021 07:58:23: 21000000 INFO @ Sat, 11 Dec 2021 07:58:26: 24000000 INFO @ Sat, 11 Dec 2021 07:58:28: 22000000 INFO @ Sat, 11 Dec 2021 07:58:31: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:58:33: 23000000 INFO @ Sat, 11 Dec 2021 07:58:37: 26000000 INFO @ Sat, 11 Dec 2021 07:58:38: 24000000 INFO @ Sat, 11 Dec 2021 07:58:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:58:42: 27000000 INFO @ Sat, 11 Dec 2021 07:58:43: 25000000 INFO @ Sat, 11 Dec 2021 07:58:48: 28000000 INFO @ Sat, 11 Dec 2021 07:58:48: 26000000 INFO @ Sat, 11 Dec 2021 07:58:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:58:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:58:48: #1 total tags in treatment: 28098208 INFO @ Sat, 11 Dec 2021 07:58:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:58:48: #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 07:58:49: #1 tags after filtering in treatment: 28098208 INFO @ Sat, 11 Dec 2021 07:58:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:58:49: #1 finished! INFO @ Sat, 11 Dec 2021 07:58:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:58:50: #2 number of paired peaks: 142 WARNING @ Sat, 11 Dec 2021 07:58:50: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sat, 11 Dec 2021 07:58:50: start model_add_line... INFO @ Sat, 11 Dec 2021 07:58:51: start X-correlation... INFO @ Sat, 11 Dec 2021 07:58:51: end of X-cor INFO @ Sat, 11 Dec 2021 07:58:51: #2 finished! INFO @ Sat, 11 Dec 2021 07:58:51: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 07:58:51: #2 alternative fragment length(s) may be 1,43,455,536,544 bps INFO @ Sat, 11 Dec 2021 07:58:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.10_model.r WARNING @ Sat, 11 Dec 2021 07:58:51: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:58:51: #2 You may need to consider one of the other alternative d(s): 1,43,455,536,544 WARNING @ Sat, 11 Dec 2021 07:58:51: #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 07:58:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:58:53: 27000000 INFO @ Sat, 11 Dec 2021 07:58:58: 28000000 INFO @ Sat, 11 Dec 2021 07:58:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:58:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:58:58: #1 total tags in treatment: 28098208 INFO @ Sat, 11 Dec 2021 07:58:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:58:58: #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 07:58:59: #1 tags after filtering in treatment: 28098208 INFO @ Sat, 11 Dec 2021 07:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:58:59: #1 finished! INFO @ Sat, 11 Dec 2021 07:58:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:59:01: #2 number of paired peaks: 142 WARNING @ Sat, 11 Dec 2021 07:59:01: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sat, 11 Dec 2021 07:59:01: start model_add_line... INFO @ Sat, 11 Dec 2021 07:59:01: start X-correlation... INFO @ Sat, 11 Dec 2021 07:59:01: end of X-cor INFO @ Sat, 11 Dec 2021 07:59:01: #2 finished! INFO @ Sat, 11 Dec 2021 07:59:01: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 07:59:01: #2 alternative fragment length(s) may be 1,43,455,536,544 bps INFO @ Sat, 11 Dec 2021 07:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.20_model.r WARNING @ Sat, 11 Dec 2021 07:59:01: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:59:01: #2 You may need to consider one of the other alternative d(s): 1,43,455,536,544 WARNING @ Sat, 11 Dec 2021 07:59:01: #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 07:59:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.05_summits.bed INFO @ Sat, 11 Dec 2021 07:59:04: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (1912 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:59:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:59:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:59:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:59:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:59:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.10_summits.bed INFO @ Sat, 11 Dec 2021 07:59:56: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (764 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:00:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:00:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:00:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434465/SRX9434465.20_summits.bed INFO @ Sat, 11 Dec 2021 08:00:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (312 records, 4 fields): 12 millis CompletedMACS2peakCalling