Job ID = 14170636 SRX = SRX9434466 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 33625544 spots for SRR12982864/SRR12982864.sra Written 33625544 spots for SRR12982864/SRR12982864.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171079 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:18 33625544 reads; of these: 33625544 (100.00%) were unpaired; of these: 715060 (2.13%) aligned 0 times 22669883 (67.42%) aligned exactly 1 time 10240601 (30.45%) aligned >1 times 97.87% overall alignment rate Time searching: 00:11:19 Overall time: 00:11:19 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] 7118765 / 32910484 = 0.2163 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 07:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.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 07:58:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:58:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:58:35: 1000000 INFO @ Sat, 11 Dec 2021 07:58:42: 2000000 INFO @ Sat, 11 Dec 2021 07:58:49: 3000000 INFO @ Sat, 11 Dec 2021 07:58:56: 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 @ Sat, 11 Dec 2021 07:58:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.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 07:58:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:58:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:59:03: 5000000 INFO @ Sat, 11 Dec 2021 07:59:06: 1000000 INFO @ Sat, 11 Dec 2021 07:59:11: 6000000 INFO @ Sat, 11 Dec 2021 07:59:13: 2000000 INFO @ Sat, 11 Dec 2021 07:59:19: 7000000 INFO @ Sat, 11 Dec 2021 07:59:21: 3000000 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 07:59:27: 8000000 INFO @ Sat, 11 Dec 2021 07:59:28: 4000000 INFO @ Sat, 11 Dec 2021 07:59:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.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 07:59:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:59:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:59:35: 9000000 INFO @ Sat, 11 Dec 2021 07:59:35: 1000000 INFO @ Sat, 11 Dec 2021 07:59:36: 5000000 INFO @ Sat, 11 Dec 2021 07:59:42: 2000000 INFO @ Sat, 11 Dec 2021 07:59:42: 10000000 INFO @ Sat, 11 Dec 2021 07:59:43: 6000000 INFO @ Sat, 11 Dec 2021 07:59:49: 3000000 INFO @ Sat, 11 Dec 2021 07:59:50: 11000000 INFO @ Sat, 11 Dec 2021 07:59:51: 7000000 INFO @ Sat, 11 Dec 2021 07:59:56: 4000000 INFO @ Sat, 11 Dec 2021 07:59:58: 12000000 INFO @ Sat, 11 Dec 2021 07:59:58: 8000000 INFO @ Sat, 11 Dec 2021 08:00:03: 5000000 INFO @ Sat, 11 Dec 2021 08:00:06: 9000000 INFO @ Sat, 11 Dec 2021 08:00:06: 13000000 INFO @ Sat, 11 Dec 2021 08:00:10: 6000000 INFO @ Sat, 11 Dec 2021 08:00:14: 10000000 INFO @ Sat, 11 Dec 2021 08:00:14: 14000000 INFO @ Sat, 11 Dec 2021 08:00:18: 7000000 INFO @ Sat, 11 Dec 2021 08:00:21: 11000000 INFO @ Sat, 11 Dec 2021 08:00:22: 15000000 INFO @ Sat, 11 Dec 2021 08:00:25: 8000000 INFO @ Sat, 11 Dec 2021 08:00:29: 12000000 INFO @ Sat, 11 Dec 2021 08:00:30: 16000000 INFO @ Sat, 11 Dec 2021 08:00:32: 9000000 INFO @ Sat, 11 Dec 2021 08:00:36: 13000000 INFO @ Sat, 11 Dec 2021 08:00:37: 17000000 INFO @ Sat, 11 Dec 2021 08:00:39: 10000000 INFO @ Sat, 11 Dec 2021 08:00:44: 14000000 INFO @ Sat, 11 Dec 2021 08:00:45: 18000000 INFO @ Sat, 11 Dec 2021 08:00:46: 11000000 INFO @ Sat, 11 Dec 2021 08:00:52: 15000000 INFO @ Sat, 11 Dec 2021 08:00:53: 19000000 INFO @ Sat, 11 Dec 2021 08:00:53: 12000000 INFO @ Sat, 11 Dec 2021 08:01:00: 16000000 INFO @ Sat, 11 Dec 2021 08:01:00: 13000000 INFO @ Sat, 11 Dec 2021 08:01:01: 20000000 INFO @ Sat, 11 Dec 2021 08:01:07: 17000000 INFO @ Sat, 11 Dec 2021 08:01:08: 14000000 INFO @ Sat, 11 Dec 2021 08:01:09: 21000000 INFO @ Sat, 11 Dec 2021 08:01:15: 15000000 INFO @ Sat, 11 Dec 2021 08:01:15: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:01:17: 22000000 INFO @ Sat, 11 Dec 2021 08:01:22: 16000000 INFO @ Sat, 11 Dec 2021 08:01:23: 19000000 INFO @ Sat, 11 Dec 2021 08:01:24: 23000000 INFO @ Sat, 11 Dec 2021 08:01:29: 17000000 INFO @ Sat, 11 Dec 2021 08:01:31: 20000000 INFO @ Sat, 11 Dec 2021 08:01:32: 24000000 INFO @ Sat, 11 Dec 2021 08:01:36: 18000000 INFO @ Sat, 11 Dec 2021 08:01:39: 21000000 INFO @ Sat, 11 Dec 2021 08:01:40: 25000000 INFO @ Sat, 11 Dec 2021 08:01:43: 19000000 INFO @ Sat, 11 Dec 2021 08:01:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:01:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:01:46: #1 total tags in treatment: 25791719 INFO @ Sat, 11 Dec 2021 08:01:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:01:46: #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 08:01:46: #1 tags after filtering in treatment: 25791719 INFO @ Sat, 11 Dec 2021 08:01:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:01:46: #1 finished! INFO @ Sat, 11 Dec 2021 08:01:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:01:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:01:46: 22000000 INFO @ Sat, 11 Dec 2021 08:01:48: #2 number of paired peaks: 142 WARNING @ Sat, 11 Dec 2021 08:01:48: 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 08:01:48: start model_add_line... INFO @ Sat, 11 Dec 2021 08:01:48: start X-correlation... INFO @ Sat, 11 Dec 2021 08:01:48: end of X-cor INFO @ Sat, 11 Dec 2021 08:01:48: #2 finished! INFO @ Sat, 11 Dec 2021 08:01:48: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 08:01:48: #2 alternative fragment length(s) may be 1,47,546 bps INFO @ Sat, 11 Dec 2021 08:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.05_model.r WARNING @ Sat, 11 Dec 2021 08:01:48: #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 08:01:48: #2 You may need to consider one of the other alternative d(s): 1,47,546 WARNING @ Sat, 11 Dec 2021 08:01:48: #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 08:01:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:01:50: 20000000 INFO @ Sat, 11 Dec 2021 08:01:54: 23000000 INFO @ Sat, 11 Dec 2021 08:01:57: 21000000 INFO @ Sat, 11 Dec 2021 08:02:02: 24000000 INFO @ Sat, 11 Dec 2021 08:02:05: 22000000 INFO @ Sat, 11 Dec 2021 08:02:09: 25000000 INFO @ Sat, 11 Dec 2021 08:02:12: 23000000 INFO @ Sat, 11 Dec 2021 08:02:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:02:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:02:15: #1 total tags in treatment: 25791719 INFO @ Sat, 11 Dec 2021 08:02:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:02:15: #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 08:02:15: #1 tags after filtering in treatment: 25791719 INFO @ Sat, 11 Dec 2021 08:02:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:02:15: #1 finished! INFO @ Sat, 11 Dec 2021 08:02:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:02:15: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:02:17: #2 number of paired peaks: 142 WARNING @ Sat, 11 Dec 2021 08:02:17: 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 08:02:17: start model_add_line... INFO @ Sat, 11 Dec 2021 08:02:17: start X-correlation... INFO @ Sat, 11 Dec 2021 08:02:17: end of X-cor INFO @ Sat, 11 Dec 2021 08:02:17: #2 finished! INFO @ Sat, 11 Dec 2021 08:02:17: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 08:02:17: #2 alternative fragment length(s) may be 1,47,546 bps INFO @ Sat, 11 Dec 2021 08:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.10_model.r WARNING @ Sat, 11 Dec 2021 08:02:17: #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 08:02:17: #2 You may need to consider one of the other alternative d(s): 1,47,546 WARNING @ Sat, 11 Dec 2021 08:02:17: #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 08:02:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:02:18: 24000000 INFO @ Sat, 11 Dec 2021 08:02:24: 25000000 INFO @ Sat, 11 Dec 2021 08:02:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:02:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:02:28: #1 total tags in treatment: 25791719 INFO @ Sat, 11 Dec 2021 08:02:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:02:28: #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 08:02:29: #1 tags after filtering in treatment: 25791719 INFO @ Sat, 11 Dec 2021 08:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:02:29: #1 finished! INFO @ Sat, 11 Dec 2021 08:02:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:02:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:02:30: #2 number of paired peaks: 142 WARNING @ Sat, 11 Dec 2021 08:02:30: 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 08:02:30: start model_add_line... INFO @ Sat, 11 Dec 2021 08:02:30: start X-correlation... INFO @ Sat, 11 Dec 2021 08:02:30: end of X-cor INFO @ Sat, 11 Dec 2021 08:02:30: #2 finished! INFO @ Sat, 11 Dec 2021 08:02:30: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 08:02:30: #2 alternative fragment length(s) may be 1,47,546 bps INFO @ Sat, 11 Dec 2021 08:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.20_model.r WARNING @ Sat, 11 Dec 2021 08:02:30: #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 08:02:30: #2 You may need to consider one of the other alternative d(s): 1,47,546 WARNING @ Sat, 11 Dec 2021 08:02:30: #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 08:02:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:02:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:02:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:02:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.05_summits.bed INFO @ Sat, 11 Dec 2021 08:02:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1855 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:03:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:03:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:03:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:03:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:03:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.10_summits.bed INFO @ Sat, 11 Dec 2021 08:03:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (786 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434466/SRX9434466.20_summits.bed INFO @ Sat, 11 Dec 2021 08:03:35: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (313 records, 4 fields): 2 millis CompletedMACS2peakCalling