Job ID = 14170579 SRX = SRX9720896 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27860188 spots for SRR13291886/SRR13291886.sra Written 27860188 spots for SRR13291886/SRR13291886.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171004 ("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: 00:10:03 27860188 reads; of these: 27860188 (100.00%) were unpaired; of these: 907025 (3.26%) aligned 0 times 18110198 (65.00%) aligned exactly 1 time 8842965 (31.74%) aligned >1 times 96.74% overall alignment rate Time searching: 00:10:03 Overall time: 00:10:03 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] 6264283 / 26953163 = 0.2324 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 07:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.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 07:35:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:35:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:35:16: 1000000 INFO @ Sat, 11 Dec 2021 07:35:22: 2000000 INFO @ Sat, 11 Dec 2021 07:35:28: 3000000 INFO @ Sat, 11 Dec 2021 07:35:34: 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 07:35:40: 5000000 INFO @ Sat, 11 Dec 2021 07:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.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 07:35:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:35:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:35:47: 6000000 INFO @ Sat, 11 Dec 2021 07:35:49: 1000000 INFO @ Sat, 11 Dec 2021 07:35:54: 7000000 INFO @ Sat, 11 Dec 2021 07:35:57: 2000000 INFO @ Sat, 11 Dec 2021 07:36:02: 8000000 INFO @ Sat, 11 Dec 2021 07:36:06: 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 07:36:09: 9000000 INFO @ Sat, 11 Dec 2021 07:36:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.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 07:36:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:36:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:36:14: 4000000 INFO @ Sat, 11 Dec 2021 07:36:17: 10000000 INFO @ Sat, 11 Dec 2021 07:36:18: 1000000 INFO @ Sat, 11 Dec 2021 07:36:22: 5000000 INFO @ Sat, 11 Dec 2021 07:36:24: 11000000 INFO @ Sat, 11 Dec 2021 07:36:25: 2000000 INFO @ Sat, 11 Dec 2021 07:36:31: 6000000 INFO @ Sat, 11 Dec 2021 07:36:31: 12000000 INFO @ Sat, 11 Dec 2021 07:36:33: 3000000 INFO @ Sat, 11 Dec 2021 07:36:39: 7000000 INFO @ Sat, 11 Dec 2021 07:36:39: 13000000 INFO @ Sat, 11 Dec 2021 07:36:40: 4000000 INFO @ Sat, 11 Dec 2021 07:36:46: 14000000 INFO @ Sat, 11 Dec 2021 07:36:47: 8000000 INFO @ Sat, 11 Dec 2021 07:36:48: 5000000 INFO @ Sat, 11 Dec 2021 07:36:54: 15000000 INFO @ Sat, 11 Dec 2021 07:36:55: 6000000 INFO @ Sat, 11 Dec 2021 07:36:55: 9000000 INFO @ Sat, 11 Dec 2021 07:37:01: 16000000 INFO @ Sat, 11 Dec 2021 07:37:02: 7000000 INFO @ Sat, 11 Dec 2021 07:37:03: 10000000 INFO @ Sat, 11 Dec 2021 07:37:09: 17000000 INFO @ Sat, 11 Dec 2021 07:37:10: 8000000 INFO @ Sat, 11 Dec 2021 07:37:11: 11000000 INFO @ Sat, 11 Dec 2021 07:37:16: 18000000 INFO @ Sat, 11 Dec 2021 07:37:17: 9000000 INFO @ Sat, 11 Dec 2021 07:37:19: 12000000 INFO @ Sat, 11 Dec 2021 07:37:24: 19000000 INFO @ Sat, 11 Dec 2021 07:37:25: 10000000 INFO @ Sat, 11 Dec 2021 07:37:27: 13000000 INFO @ Sat, 11 Dec 2021 07:37:31: 20000000 INFO @ Sat, 11 Dec 2021 07:37:32: 11000000 INFO @ Sat, 11 Dec 2021 07:37:36: 14000000 INFO @ Sat, 11 Dec 2021 07:37:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:37:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:37:36: #1 total tags in treatment: 20688880 INFO @ Sat, 11 Dec 2021 07:37:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:37:36: #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 07:37:37: #1 tags after filtering in treatment: 20688880 INFO @ Sat, 11 Dec 2021 07:37:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:37:37: #1 finished! INFO @ Sat, 11 Dec 2021 07:37:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:37:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:37:38: #2 number of paired peaks: 482 WARNING @ Sat, 11 Dec 2021 07:37:38: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sat, 11 Dec 2021 07:37:38: start model_add_line... BedGraph に変換しました。 INFO @ Sat, 11 Dec 2021 07:37:38: start X-correlation... BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:37:38: end of X-cor INFO @ Sat, 11 Dec 2021 07:37:38: #2 finished! INFO @ Sat, 11 Dec 2021 07:37:38: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 07:37:38: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 11 Dec 2021 07:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.05_model.r WARNING @ Sat, 11 Dec 2021 07:37:38: #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 07:37:38: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 11 Dec 2021 07:37:38: #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 07:37:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:37:39: 12000000 INFO @ Sat, 11 Dec 2021 07:37:44: 15000000 INFO @ Sat, 11 Dec 2021 07:37:47: 13000000 INFO @ Sat, 11 Dec 2021 07:37:52: 16000000 INFO @ Sat, 11 Dec 2021 07:37:54: 14000000 INFO @ Sat, 11 Dec 2021 07:38:00: 17000000 INFO @ Sat, 11 Dec 2021 07:38:02: 15000000 INFO @ Sat, 11 Dec 2021 07:38:08: 18000000 INFO @ Sat, 11 Dec 2021 07:38:09: 16000000 INFO @ Sat, 11 Dec 2021 07:38:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:38:16: 19000000 INFO @ Sat, 11 Dec 2021 07:38:16: 17000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:38:24: 18000000 INFO @ Sat, 11 Dec 2021 07:38:24: 20000000 INFO @ Sat, 11 Dec 2021 07:38:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:38:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:38:29: #1 total tags in treatment: 20688880 INFO @ Sat, 11 Dec 2021 07:38:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:38:29: #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 07:38:30: #1 tags after filtering in treatment: 20688880 INFO @ Sat, 11 Dec 2021 07:38:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:38:30: #1 finished! INFO @ Sat, 11 Dec 2021 07:38:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:38:31: #2 number of paired peaks: 482 WARNING @ Sat, 11 Dec 2021 07:38:31: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sat, 11 Dec 2021 07:38:31: start model_add_line... INFO @ Sat, 11 Dec 2021 07:38:31: 19000000 INFO @ Sat, 11 Dec 2021 07:38:31: start X-correlation... INFO @ Sat, 11 Dec 2021 07:38:31: end of X-cor INFO @ Sat, 11 Dec 2021 07:38:31: #2 finished! INFO @ Sat, 11 Dec 2021 07:38:31: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 07:38:31: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 11 Dec 2021 07:38:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.10_model.r WARNING @ Sat, 11 Dec 2021 07:38:31: #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 07:38:31: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 11 Dec 2021 07:38:31: #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 07:38:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:38:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.05_summits.bed INFO @ Sat, 11 Dec 2021 07:38:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3665 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:38:37: 20000000 INFO @ Sat, 11 Dec 2021 07:38:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:38:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:38:41: #1 total tags in treatment: 20688880 INFO @ Sat, 11 Dec 2021 07:38:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:38:41: #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 07:38:41: #1 tags after filtering in treatment: 20688880 INFO @ Sat, 11 Dec 2021 07:38:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:38:41: #1 finished! INFO @ Sat, 11 Dec 2021 07:38:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:38:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:38:42: #2 number of paired peaks: 482 WARNING @ Sat, 11 Dec 2021 07:38:42: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sat, 11 Dec 2021 07:38:42: start model_add_line... INFO @ Sat, 11 Dec 2021 07:38:43: start X-correlation... INFO @ Sat, 11 Dec 2021 07:38:43: end of X-cor INFO @ Sat, 11 Dec 2021 07:38:43: #2 finished! INFO @ Sat, 11 Dec 2021 07:38:43: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 07:38:43: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 11 Dec 2021 07:38:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.20_model.r WARNING @ Sat, 11 Dec 2021 07:38:43: #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 07:38:43: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 11 Dec 2021 07:38:43: #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 07:38:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:38:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:39:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:39:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:39:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:39:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:39:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.10_summits.bed INFO @ Sat, 11 Dec 2021 07:39:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2578 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720896/SRX9720896.20_summits.bed INFO @ Sat, 11 Dec 2021 07:39:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1332 records, 4 fields): 4 millis CompletedMACS2peakCalling