Job ID = 14170366 SRX = SRX9720901 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25426755 spots for SRR13291891/SRR13291891.sra Written 25426755 spots for SRR13291891/SRR13291891.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170765 ("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: 00:08:42 25426755 reads; of these: 25426755 (100.00%) were unpaired; of these: 992340 (3.90%) aligned 0 times 16829591 (66.19%) aligned exactly 1 time 7604824 (29.91%) aligned >1 times 96.10% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 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 12 files... [bam_rmdupse_core] 4381202 / 24434415 = 0.1793 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 06:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.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 06:36:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:36:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:36:48: 1000000 INFO @ Sat, 11 Dec 2021 06:36:54: 2000000 INFO @ Sat, 11 Dec 2021 06:37:00: 3000000 INFO @ Sat, 11 Dec 2021 06:37:06: 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 06:37:12: 5000000 INFO @ Sat, 11 Dec 2021 06:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.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 06:37:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:37:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:37:17: 1000000 INFO @ Sat, 11 Dec 2021 06:37:18: 6000000 INFO @ Sat, 11 Dec 2021 06:37:23: 2000000 INFO @ Sat, 11 Dec 2021 06:37:25: 7000000 INFO @ Sat, 11 Dec 2021 06:37:28: 3000000 INFO @ Sat, 11 Dec 2021 06:37:31: 8000000 INFO @ Sat, 11 Dec 2021 06:37:34: 4000000 INFO @ Sat, 11 Dec 2021 06:37:37: 9000000 INFO @ Sat, 11 Dec 2021 06:37:39: 5000000 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 06:37:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.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 06:37:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:37:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:37:44: 10000000 INFO @ Sat, 11 Dec 2021 06:37:45: 6000000 INFO @ Sat, 11 Dec 2021 06:37:48: 1000000 INFO @ Sat, 11 Dec 2021 06:37:50: 11000000 INFO @ Sat, 11 Dec 2021 06:37:50: 7000000 INFO @ Sat, 11 Dec 2021 06:37:55: 2000000 INFO @ Sat, 11 Dec 2021 06:37:55: 8000000 INFO @ Sat, 11 Dec 2021 06:37:56: 12000000 INFO @ Sat, 11 Dec 2021 06:38:01: 9000000 INFO @ Sat, 11 Dec 2021 06:38:01: 3000000 INFO @ Sat, 11 Dec 2021 06:38:03: 13000000 INFO @ Sat, 11 Dec 2021 06:38:06: 10000000 INFO @ Sat, 11 Dec 2021 06:38:07: 4000000 INFO @ Sat, 11 Dec 2021 06:38:09: 14000000 INFO @ Sat, 11 Dec 2021 06:38:12: 11000000 INFO @ Sat, 11 Dec 2021 06:38:14: 5000000 INFO @ Sat, 11 Dec 2021 06:38:15: 15000000 INFO @ Sat, 11 Dec 2021 06:38:17: 12000000 INFO @ Sat, 11 Dec 2021 06:38:20: 6000000 INFO @ Sat, 11 Dec 2021 06:38:22: 16000000 INFO @ Sat, 11 Dec 2021 06:38:23: 13000000 INFO @ Sat, 11 Dec 2021 06:38:26: 7000000 INFO @ Sat, 11 Dec 2021 06:38:28: 17000000 INFO @ Sat, 11 Dec 2021 06:38:28: 14000000 INFO @ Sat, 11 Dec 2021 06:38:33: 8000000 INFO @ Sat, 11 Dec 2021 06:38:34: 15000000 INFO @ Sat, 11 Dec 2021 06:38:34: 18000000 INFO @ Sat, 11 Dec 2021 06:38:39: 9000000 INFO @ Sat, 11 Dec 2021 06:38:39: 16000000 INFO @ Sat, 11 Dec 2021 06:38:40: 19000000 INFO @ Sat, 11 Dec 2021 06:38:45: 17000000 INFO @ Sat, 11 Dec 2021 06:38:45: 10000000 INFO @ Sat, 11 Dec 2021 06:38:46: 20000000 INFO @ Sat, 11 Dec 2021 06:38:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:38:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:38:46: #1 total tags in treatment: 20053213 INFO @ Sat, 11 Dec 2021 06:38:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:38:46: #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 06:38:47: #1 tags after filtering in treatment: 20053213 INFO @ Sat, 11 Dec 2021 06:38:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:38:47: #1 finished! INFO @ Sat, 11 Dec 2021 06:38:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:38:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:38:48: #2 number of paired peaks: 442 WARNING @ Sat, 11 Dec 2021 06:38:48: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Sat, 11 Dec 2021 06:38:48: start model_add_line... INFO @ Sat, 11 Dec 2021 06:38:48: start X-correlation... INFO @ Sat, 11 Dec 2021 06:38:48: end of X-cor INFO @ Sat, 11 Dec 2021 06:38:48: #2 finished! INFO @ Sat, 11 Dec 2021 06:38:48: #2 predicted fragment length is 63 bps INFO @ Sat, 11 Dec 2021 06:38:48: #2 alternative fragment length(s) may be 63 bps INFO @ Sat, 11 Dec 2021 06:38:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.05_model.r WARNING @ Sat, 11 Dec 2021 06:38:48: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:38:48: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sat, 11 Dec 2021 06:38:48: #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 06:38:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:38:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:38:50: 18000000 INFO @ Sat, 11 Dec 2021 06:38:52: 11000000 INFO @ Sat, 11 Dec 2021 06:38:56: 19000000 INFO @ Sat, 11 Dec 2021 06:38:58: 12000000 INFO @ Sat, 11 Dec 2021 06:39:01: 20000000 INFO @ Sat, 11 Dec 2021 06:39:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:39:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:39:02: #1 total tags in treatment: 20053213 INFO @ Sat, 11 Dec 2021 06:39:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:39:02: #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 06:39:02: #1 tags after filtering in treatment: 20053213 INFO @ Sat, 11 Dec 2021 06:39:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:39:02: #1 finished! INFO @ Sat, 11 Dec 2021 06:39:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:39:03: #2 number of paired peaks: 442 WARNING @ Sat, 11 Dec 2021 06:39:03: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Sat, 11 Dec 2021 06:39:03: start model_add_line... INFO @ Sat, 11 Dec 2021 06:39:03: start X-correlation... INFO @ Sat, 11 Dec 2021 06:39:03: end of X-cor INFO @ Sat, 11 Dec 2021 06:39:03: #2 finished! INFO @ Sat, 11 Dec 2021 06:39:03: #2 predicted fragment length is 63 bps INFO @ Sat, 11 Dec 2021 06:39:03: #2 alternative fragment length(s) may be 63 bps INFO @ Sat, 11 Dec 2021 06:39:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.10_model.r WARNING @ Sat, 11 Dec 2021 06:39:03: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:39:03: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sat, 11 Dec 2021 06:39:03: #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 06:39:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:39:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:39:04: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:39:10: 14000000 INFO @ Sat, 11 Dec 2021 06:39:16: 15000000 INFO @ Sat, 11 Dec 2021 06:39:22: 16000000 INFO @ Sat, 11 Dec 2021 06:39:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:39:28: 17000000 INFO @ Sat, 11 Dec 2021 06:39:34: 18000000 INFO @ Sat, 11 Dec 2021 06:39:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:39:40: 19000000 INFO @ Sat, 11 Dec 2021 06:39:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:39:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:39:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.05_summits.bed INFO @ Sat, 11 Dec 2021 06:39:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4658 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:39:46: 20000000 INFO @ Sat, 11 Dec 2021 06:39:47: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:39:47: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:39:47: #1 total tags in treatment: 20053213 INFO @ Sat, 11 Dec 2021 06:39:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:39:47: #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 06:39:47: #1 tags after filtering in treatment: 20053213 INFO @ Sat, 11 Dec 2021 06:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:39:47: #1 finished! INFO @ Sat, 11 Dec 2021 06:39:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:39:48: #2 number of paired peaks: 442 WARNING @ Sat, 11 Dec 2021 06:39:48: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Sat, 11 Dec 2021 06:39:48: start model_add_line... INFO @ Sat, 11 Dec 2021 06:39:48: start X-correlation... INFO @ Sat, 11 Dec 2021 06:39:48: end of X-cor INFO @ Sat, 11 Dec 2021 06:39:48: #2 finished! INFO @ Sat, 11 Dec 2021 06:39:48: #2 predicted fragment length is 63 bps INFO @ Sat, 11 Dec 2021 06:39:48: #2 alternative fragment length(s) may be 63 bps INFO @ Sat, 11 Dec 2021 06:39:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.20_model.r WARNING @ Sat, 11 Dec 2021 06:39:48: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:39:48: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sat, 11 Dec 2021 06:39:48: #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 06:39:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:39:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.10_summits.bed INFO @ Sat, 11 Dec 2021 06:39:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3063 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:40:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:40:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:40:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:40:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720901/SRX9720901.20_summits.bed INFO @ Sat, 11 Dec 2021 06:40:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1677 records, 4 fields): 3 millis CompletedMACS2peakCalling