Job ID = 14170625 SRX = SRX9434463 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 39741127 spots for SRR12982861/SRR12982861.sra Written 39741127 spots for SRR12982861/SRR12982861.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171072 ("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: 00:13:42 39741127 reads; of these: 39741127 (100.00%) were unpaired; of these: 853605 (2.15%) aligned 0 times 26570076 (66.86%) aligned exactly 1 time 12317446 (30.99%) aligned >1 times 97.85% overall alignment rate Time searching: 00:13:42 Overall time: 00:13:42 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] 9198360 / 38887522 = 0.2365 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 07:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.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 07:57:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:57:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:57:06: 1000000 INFO @ Sat, 11 Dec 2021 07:57:11: 2000000 INFO @ Sat, 11 Dec 2021 07:57:15: 3000000 INFO @ Sat, 11 Dec 2021 07:57:20: 4000000 INFO @ Sat, 11 Dec 2021 07:57:25: 5000000 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 07:57:29: 6000000 INFO @ Sat, 11 Dec 2021 07:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.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 07:57:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:57:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:57:34: 7000000 INFO @ Sat, 11 Dec 2021 07:57:36: 1000000 INFO @ Sat, 11 Dec 2021 07:57:39: 8000000 INFO @ Sat, 11 Dec 2021 07:57:40: 2000000 INFO @ Sat, 11 Dec 2021 07:57:44: 9000000 INFO @ Sat, 11 Dec 2021 07:57:45: 3000000 INFO @ Sat, 11 Dec 2021 07:57:48: 10000000 INFO @ Sat, 11 Dec 2021 07:57:50: 4000000 INFO @ Sat, 11 Dec 2021 07:57:53: 11000000 INFO @ Sat, 11 Dec 2021 07:57:54: 5000000 INFO @ Sat, 11 Dec 2021 07:57:58: 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 07:57:59: 6000000 INFO @ Sat, 11 Dec 2021 07:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.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 07:58:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:58:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:58:03: 13000000 INFO @ Sat, 11 Dec 2021 07:58:04: 7000000 INFO @ Sat, 11 Dec 2021 07:58:06: 1000000 INFO @ Sat, 11 Dec 2021 07:58:08: 14000000 INFO @ Sat, 11 Dec 2021 07:58:09: 8000000 INFO @ Sat, 11 Dec 2021 07:58:11: 2000000 INFO @ Sat, 11 Dec 2021 07:58:13: 15000000 INFO @ Sat, 11 Dec 2021 07:58:13: 9000000 INFO @ Sat, 11 Dec 2021 07:58:17: 3000000 INFO @ Sat, 11 Dec 2021 07:58:18: 16000000 INFO @ Sat, 11 Dec 2021 07:58:18: 10000000 INFO @ Sat, 11 Dec 2021 07:58:22: 4000000 INFO @ Sat, 11 Dec 2021 07:58:23: 17000000 INFO @ Sat, 11 Dec 2021 07:58:23: 11000000 INFO @ Sat, 11 Dec 2021 07:58:27: 5000000 INFO @ Sat, 11 Dec 2021 07:58:28: 18000000 INFO @ Sat, 11 Dec 2021 07:58:28: 12000000 INFO @ Sat, 11 Dec 2021 07:58:32: 13000000 INFO @ Sat, 11 Dec 2021 07:58:32: 19000000 INFO @ Sat, 11 Dec 2021 07:58:33: 6000000 INFO @ Sat, 11 Dec 2021 07:58:37: 14000000 INFO @ Sat, 11 Dec 2021 07:58:37: 20000000 INFO @ Sat, 11 Dec 2021 07:58:38: 7000000 INFO @ Sat, 11 Dec 2021 07:58:42: 15000000 INFO @ Sat, 11 Dec 2021 07:58:42: 21000000 INFO @ Sat, 11 Dec 2021 07:58:43: 8000000 INFO @ Sat, 11 Dec 2021 07:58:46: 16000000 INFO @ Sat, 11 Dec 2021 07:58:47: 22000000 INFO @ Sat, 11 Dec 2021 07:58:49: 9000000 INFO @ Sat, 11 Dec 2021 07:58:51: 17000000 INFO @ Sat, 11 Dec 2021 07:58:52: 23000000 INFO @ Sat, 11 Dec 2021 07:58:54: 10000000 INFO @ Sat, 11 Dec 2021 07:58:56: 18000000 INFO @ Sat, 11 Dec 2021 07:58:57: 24000000 INFO @ Sat, 11 Dec 2021 07:58:59: 11000000 INFO @ Sat, 11 Dec 2021 07:59:00: 19000000 INFO @ Sat, 11 Dec 2021 07:59:02: 25000000 INFO @ Sat, 11 Dec 2021 07:59:05: 12000000 INFO @ Sat, 11 Dec 2021 07:59:05: 20000000 INFO @ Sat, 11 Dec 2021 07:59:07: 26000000 INFO @ Sat, 11 Dec 2021 07:59:09: 13000000 INFO @ Sat, 11 Dec 2021 07:59:10: 21000000 INFO @ Sat, 11 Dec 2021 07:59:12: 27000000 INFO @ Sat, 11 Dec 2021 07:59:14: 14000000 INFO @ Sat, 11 Dec 2021 07:59:14: 22000000 INFO @ Sat, 11 Dec 2021 07:59:17: 28000000 INFO @ Sat, 11 Dec 2021 07:59:19: 15000000 INFO @ Sat, 11 Dec 2021 07:59:19: 23000000 INFO @ Sat, 11 Dec 2021 07:59:22: 29000000 INFO @ Sat, 11 Dec 2021 07:59:24: 24000000 INFO @ Sat, 11 Dec 2021 07:59:24: 16000000 INFO @ Sat, 11 Dec 2021 07:59:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:59:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:59:26: #1 total tags in treatment: 29689162 INFO @ Sat, 11 Dec 2021 07:59:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:59:26: #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 07:59:26: #1 tags after filtering in treatment: 29689162 INFO @ Sat, 11 Dec 2021 07:59:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:59:26: #1 finished! INFO @ Sat, 11 Dec 2021 07:59:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:59:28: #2 number of paired peaks: 135 WARNING @ Sat, 11 Dec 2021 07:59:28: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 11 Dec 2021 07:59:28: start model_add_line... INFO @ Sat, 11 Dec 2021 07:59:28: start X-correlation... INFO @ Sat, 11 Dec 2021 07:59:28: end of X-cor INFO @ Sat, 11 Dec 2021 07:59:28: #2 finished! INFO @ Sat, 11 Dec 2021 07:59:28: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 07:59:28: #2 alternative fragment length(s) may be 1,47,513 bps INFO @ Sat, 11 Dec 2021 07:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.05_model.r WARNING @ Sat, 11 Dec 2021 07:59:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:59:28: #2 You may need to consider one of the other alternative d(s): 1,47,513 WARNING @ Sat, 11 Dec 2021 07:59:28: #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 07:59:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:59:29: 25000000 INFO @ Sat, 11 Dec 2021 07:59:30: 17000000 INFO @ Sat, 11 Dec 2021 07:59:33: 26000000 INFO @ Sat, 11 Dec 2021 07:59:35: 18000000 INFO @ Sat, 11 Dec 2021 07:59:38: 27000000 INFO @ Sat, 11 Dec 2021 07:59:41: 19000000 INFO @ Sat, 11 Dec 2021 07:59:43: 28000000 INFO @ Sat, 11 Dec 2021 07:59:46: 20000000 INFO @ Sat, 11 Dec 2021 07:59:47: 29000000 INFO @ Sat, 11 Dec 2021 07:59:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:59:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:59:51: #1 total tags in treatment: 29689162 INFO @ Sat, 11 Dec 2021 07:59:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:59:51: #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 07:59:51: #1 tags after filtering in treatment: 29689162 INFO @ Sat, 11 Dec 2021 07:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:59:51: #1 finished! INFO @ Sat, 11 Dec 2021 07:59:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:59:51: 21000000 INFO @ Sat, 11 Dec 2021 07:59:53: #2 number of paired peaks: 135 WARNING @ Sat, 11 Dec 2021 07:59:53: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 11 Dec 2021 07:59:53: start model_add_line... INFO @ Sat, 11 Dec 2021 07:59:53: start X-correlation... INFO @ Sat, 11 Dec 2021 07:59:53: end of X-cor INFO @ Sat, 11 Dec 2021 07:59:53: #2 finished! INFO @ Sat, 11 Dec 2021 07:59:53: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 07:59:53: #2 alternative fragment length(s) may be 1,47,513 bps INFO @ Sat, 11 Dec 2021 07:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.10_model.r WARNING @ Sat, 11 Dec 2021 07:59:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:59:53: #2 You may need to consider one of the other alternative d(s): 1,47,513 WARNING @ Sat, 11 Dec 2021 07:59:53: #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 07:59:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:59:57: 22000000 INFO @ Sat, 11 Dec 2021 08:00:02: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:00:07: 24000000 INFO @ Sat, 11 Dec 2021 08:00:12: 25000000 INFO @ Sat, 11 Dec 2021 08:00:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:00:18: 26000000 INFO @ Sat, 11 Dec 2021 08:00:23: 27000000 INFO @ Sat, 11 Dec 2021 08:00:28: 28000000 INFO @ Sat, 11 Dec 2021 08:00:34: 29000000 INFO @ Sat, 11 Dec 2021 08:00:37: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:00:37: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:00:37: #1 total tags in treatment: 29689162 INFO @ Sat, 11 Dec 2021 08:00:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:00:37: #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 08:00:38: #1 tags after filtering in treatment: 29689162 INFO @ Sat, 11 Dec 2021 08:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:00:38: #1 finished! INFO @ Sat, 11 Dec 2021 08:00:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:00:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:00:40: #2 number of paired peaks: 135 WARNING @ Sat, 11 Dec 2021 08:00:40: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 11 Dec 2021 08:00:40: start model_add_line... INFO @ Sat, 11 Dec 2021 08:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:00:40: start X-correlation... INFO @ Sat, 11 Dec 2021 08:00:40: end of X-cor INFO @ Sat, 11 Dec 2021 08:00:40: #2 finished! INFO @ Sat, 11 Dec 2021 08:00:40: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 08:00:40: #2 alternative fragment length(s) may be 1,47,513 bps INFO @ Sat, 11 Dec 2021 08:00:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.20_model.r INFO @ Sat, 11 Dec 2021 08:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.05_peaks.narrowPeak WARNING @ Sat, 11 Dec 2021 08:00:40: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:00:40: #2 You may need to consider one of the other alternative d(s): 1,47,513 WARNING @ Sat, 11 Dec 2021 08:00:40: #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 08:00:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:00:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.05_summits.bed INFO @ Sat, 11 Dec 2021 08:00:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2209 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.10_summits.bed INFO @ Sat, 11 Dec 2021 08:01:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (837 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:01:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434463/SRX9434463.20_summits.bed INFO @ Sat, 11 Dec 2021 08:01:51: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (349 records, 4 fields): 2 millis CompletedMACS2peakCalling