Job ID = 14171869 SRX = SRX3292994 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24780645 spots for SRR6182820/SRR6182820.sra Written 24780645 spots for SRR6182820/SRR6182820.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172390 ("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: 00:13:15 24780645 reads; of these: 24780645 (100.00%) were unpaired; of these: 2580949 (10.42%) aligned 0 times 17191716 (69.38%) aligned exactly 1 time 5007980 (20.21%) aligned >1 times 89.58% overall alignment rate Time searching: 00:13:15 Overall time: 00:13:15 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] 3041715 / 22199696 = 0.1370 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 13:38:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.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 13:38:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:38:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:38:12: 1000000 INFO @ Sat, 11 Dec 2021 13:38:19: 2000000 INFO @ Sat, 11 Dec 2021 13:38:25: 3000000 INFO @ Sat, 11 Dec 2021 13:38:32: 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 13:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.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 13:38:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:38:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:38:39: 5000000 INFO @ Sat, 11 Dec 2021 13:38:45: 1000000 INFO @ Sat, 11 Dec 2021 13:38:48: 6000000 INFO @ Sat, 11 Dec 2021 13:38:54: 2000000 INFO @ Sat, 11 Dec 2021 13:38:56: 7000000 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 13:39:04: 3000000 INFO @ Sat, 11 Dec 2021 13:39:04: 8000000 INFO @ Sat, 11 Dec 2021 13:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.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 13:39:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:39:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:39:12: 9000000 INFO @ Sat, 11 Dec 2021 13:39:13: 4000000 INFO @ Sat, 11 Dec 2021 13:39:14: 1000000 INFO @ Sat, 11 Dec 2021 13:39:21: 10000000 INFO @ Sat, 11 Dec 2021 13:39:22: 2000000 INFO @ Sat, 11 Dec 2021 13:39:23: 5000000 INFO @ Sat, 11 Dec 2021 13:39:29: 11000000 INFO @ Sat, 11 Dec 2021 13:39:30: 3000000 INFO @ Sat, 11 Dec 2021 13:39:32: 6000000 INFO @ Sat, 11 Dec 2021 13:39:37: 12000000 INFO @ Sat, 11 Dec 2021 13:39:39: 4000000 INFO @ Sat, 11 Dec 2021 13:39:41: 7000000 INFO @ Sat, 11 Dec 2021 13:39:46: 13000000 INFO @ Sat, 11 Dec 2021 13:39:47: 5000000 INFO @ Sat, 11 Dec 2021 13:39:50: 8000000 INFO @ Sat, 11 Dec 2021 13:39:54: 14000000 INFO @ Sat, 11 Dec 2021 13:39:56: 6000000 INFO @ Sat, 11 Dec 2021 13:39:59: 9000000 INFO @ Sat, 11 Dec 2021 13:40:02: 15000000 INFO @ Sat, 11 Dec 2021 13:40:04: 7000000 INFO @ Sat, 11 Dec 2021 13:40:09: 10000000 INFO @ Sat, 11 Dec 2021 13:40:11: 16000000 INFO @ Sat, 11 Dec 2021 13:40:12: 8000000 INFO @ Sat, 11 Dec 2021 13:40:17: 11000000 INFO @ Sat, 11 Dec 2021 13:40:19: 17000000 INFO @ Sat, 11 Dec 2021 13:40:21: 9000000 INFO @ Sat, 11 Dec 2021 13:40:27: 12000000 INFO @ Sat, 11 Dec 2021 13:40:28: 18000000 INFO @ Sat, 11 Dec 2021 13:40:29: 10000000 INFO @ Sat, 11 Dec 2021 13:40:36: 19000000 INFO @ Sat, 11 Dec 2021 13:40:36: 13000000 INFO @ Sat, 11 Dec 2021 13:40:37: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:40:37: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:40:37: #1 total tags in treatment: 19157981 INFO @ Sat, 11 Dec 2021 13:40:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:40:37: #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 13:40:37: 11000000 INFO @ Sat, 11 Dec 2021 13:40:38: #1 tags after filtering in treatment: 19157981 INFO @ Sat, 11 Dec 2021 13:40:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:40:38: #1 finished! INFO @ Sat, 11 Dec 2021 13:40:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:40:39: #2 number of paired peaks: 157 WARNING @ Sat, 11 Dec 2021 13:40:39: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 11 Dec 2021 13:40:39: start model_add_line... INFO @ Sat, 11 Dec 2021 13:40:39: start X-correlation... INFO @ Sat, 11 Dec 2021 13:40:39: end of X-cor INFO @ Sat, 11 Dec 2021 13:40:39: #2 finished! INFO @ Sat, 11 Dec 2021 13:40:39: #2 predicted fragment length is 120 bps INFO @ Sat, 11 Dec 2021 13:40:39: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sat, 11 Dec 2021 13:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.05_model.r WARNING @ Sat, 11 Dec 2021 13:40:39: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:40:39: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sat, 11 Dec 2021 13:40:39: #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 13:40:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:40:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:40:45: 14000000 INFO @ Sat, 11 Dec 2021 13:40:46: 12000000 INFO @ Sat, 11 Dec 2021 13:40:54: 13000000 INFO @ Sat, 11 Dec 2021 13:40:55: 15000000 INFO @ Sat, 11 Dec 2021 13:41:02: 14000000 INFO @ Sat, 11 Dec 2021 13:41:04: 16000000 INFO @ Sat, 11 Dec 2021 13:41:10: 15000000 INFO @ Sat, 11 Dec 2021 13:41:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:41:14: 17000000 INFO @ Sat, 11 Dec 2021 13:41:19: 16000000 INFO @ Sat, 11 Dec 2021 13:41:24: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:41:27: 17000000 INFO @ Sat, 11 Dec 2021 13:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.05_summits.bed INFO @ Sat, 11 Dec 2021 13:41:31: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1755 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:41:33: 19000000 INFO @ Sat, 11 Dec 2021 13:41:35: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:41:35: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:41:35: #1 total tags in treatment: 19157981 INFO @ Sat, 11 Dec 2021 13:41:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:41:35: #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 13:41:35: 18000000 INFO @ Sat, 11 Dec 2021 13:41:35: #1 tags after filtering in treatment: 19157981 INFO @ Sat, 11 Dec 2021 13:41:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:41:35: #1 finished! INFO @ Sat, 11 Dec 2021 13:41:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:41:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:41:36: #2 number of paired peaks: 157 WARNING @ Sat, 11 Dec 2021 13:41:36: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 11 Dec 2021 13:41:36: start model_add_line... INFO @ Sat, 11 Dec 2021 13:41:36: start X-correlation... INFO @ Sat, 11 Dec 2021 13:41:36: end of X-cor INFO @ Sat, 11 Dec 2021 13:41:36: #2 finished! INFO @ Sat, 11 Dec 2021 13:41:36: #2 predicted fragment length is 120 bps INFO @ Sat, 11 Dec 2021 13:41:36: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sat, 11 Dec 2021 13:41:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.10_model.r WARNING @ Sat, 11 Dec 2021 13:41:36: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:41:36: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sat, 11 Dec 2021 13:41:36: #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 13:41:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:41:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:41:43: 19000000 INFO @ Sat, 11 Dec 2021 13:41:44: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:41:44: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:41:44: #1 total tags in treatment: 19157981 INFO @ Sat, 11 Dec 2021 13:41:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:41:44: #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 13:41:44: #1 tags after filtering in treatment: 19157981 INFO @ Sat, 11 Dec 2021 13:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:41:44: #1 finished! INFO @ Sat, 11 Dec 2021 13:41:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:41:45: #2 number of paired peaks: 157 WARNING @ Sat, 11 Dec 2021 13:41:45: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 11 Dec 2021 13:41:45: start model_add_line... INFO @ Sat, 11 Dec 2021 13:41:45: start X-correlation... INFO @ Sat, 11 Dec 2021 13:41:45: end of X-cor INFO @ Sat, 11 Dec 2021 13:41:45: #2 finished! INFO @ Sat, 11 Dec 2021 13:41:45: #2 predicted fragment length is 120 bps INFO @ Sat, 11 Dec 2021 13:41:45: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sat, 11 Dec 2021 13:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.20_model.r WARNING @ Sat, 11 Dec 2021 13:41:45: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:41:45: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sat, 11 Dec 2021 13:41:45: #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 13:41:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:42:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:42:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:42:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.10_summits.bed INFO @ Sat, 11 Dec 2021 13:42:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (924 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:42:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3292994/SRX3292994.20_summits.bed INFO @ Sat, 11 Dec 2021 13:42:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 2 millis CompletedMACS2peakCalling