Job ID = 14167040 SRX = SRX8694697 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29815307 spots for SRR12180111/SRR12180111.sra Written 29815307 spots for SRR12180111/SRR12180111.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167611 ("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: 01:21:31 29815307 reads; of these: 29815307 (100.00%) were paired; of these: 10963190 (36.77%) aligned concordantly 0 times 13775216 (46.20%) aligned concordantly exactly 1 time 5076901 (17.03%) aligned concordantly >1 times ---- 10963190 pairs aligned concordantly 0 times; of these: 1953782 (17.82%) aligned discordantly 1 time ---- 9009408 pairs aligned 0 times concordantly or discordantly; of these: 18018816 mates make up the pairs; of these: 15315313 (85.00%) aligned 0 times 936142 (5.20%) aligned exactly 1 time 1767361 (9.81%) aligned >1 times 74.32% overall alignment rate Time searching: 01:21:32 Overall time: 01:21:32 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 36 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4180199 / 20633335 = 0.2026 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 @ Fri, 10 Dec 2021 10:47:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.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 @ Fri, 10 Dec 2021 10:47:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:47:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:48:06: 1000000 INFO @ Fri, 10 Dec 2021 10:48:13: 2000000 INFO @ Fri, 10 Dec 2021 10:48:21: 3000000 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 @ Fri, 10 Dec 2021 10:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.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 @ Fri, 10 Dec 2021 10:48:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:48:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:48:28: 4000000 INFO @ Fri, 10 Dec 2021 10:48:38: 5000000 INFO @ Fri, 10 Dec 2021 10:48:39: 1000000 INFO @ Fri, 10 Dec 2021 10:48:47: 6000000 INFO @ Fri, 10 Dec 2021 10:48:50: 2000000 INFO @ Fri, 10 Dec 2021 10:48:56: 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 @ Fri, 10 Dec 2021 10:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.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 @ Fri, 10 Dec 2021 10:48:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:48:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:49:01: 3000000 INFO @ Fri, 10 Dec 2021 10:49:06: 8000000 INFO @ Fri, 10 Dec 2021 10:49:08: 1000000 INFO @ Fri, 10 Dec 2021 10:49:12: 4000000 INFO @ Fri, 10 Dec 2021 10:49:16: 9000000 INFO @ Fri, 10 Dec 2021 10:49:18: 2000000 INFO @ Fri, 10 Dec 2021 10:49:24: 5000000 INFO @ Fri, 10 Dec 2021 10:49:25: 10000000 INFO @ Fri, 10 Dec 2021 10:49:28: 3000000 INFO @ Fri, 10 Dec 2021 10:49:35: 11000000 INFO @ Fri, 10 Dec 2021 10:49:36: 6000000 INFO @ Fri, 10 Dec 2021 10:49:37: 4000000 INFO @ Fri, 10 Dec 2021 10:49:45: 12000000 INFO @ Fri, 10 Dec 2021 10:49:47: 5000000 INFO @ Fri, 10 Dec 2021 10:49:48: 7000000 INFO @ Fri, 10 Dec 2021 10:49:55: 13000000 INFO @ Fri, 10 Dec 2021 10:49:57: 6000000 INFO @ Fri, 10 Dec 2021 10:49:59: 8000000 INFO @ Fri, 10 Dec 2021 10:50:05: 14000000 INFO @ Fri, 10 Dec 2021 10:50:07: 7000000 INFO @ Fri, 10 Dec 2021 10:50:12: 9000000 INFO @ Fri, 10 Dec 2021 10:50:15: 15000000 INFO @ Fri, 10 Dec 2021 10:50:16: 8000000 INFO @ Fri, 10 Dec 2021 10:50:23: 10000000 INFO @ Fri, 10 Dec 2021 10:50:25: 16000000 INFO @ Fri, 10 Dec 2021 10:50:26: 9000000 INFO @ Fri, 10 Dec 2021 10:50:35: 17000000 INFO @ Fri, 10 Dec 2021 10:50:35: 11000000 INFO @ Fri, 10 Dec 2021 10:50:36: 10000000 INFO @ Fri, 10 Dec 2021 10:50:44: 18000000 INFO @ Fri, 10 Dec 2021 10:50:46: 12000000 INFO @ Fri, 10 Dec 2021 10:50:46: 11000000 INFO @ Fri, 10 Dec 2021 10:50:54: 19000000 INFO @ Fri, 10 Dec 2021 10:50:56: 12000000 INFO @ Fri, 10 Dec 2021 10:50:57: 13000000 INFO @ Fri, 10 Dec 2021 10:51:04: 20000000 INFO @ Fri, 10 Dec 2021 10:51:06: 13000000 INFO @ Fri, 10 Dec 2021 10:51:08: 14000000 INFO @ Fri, 10 Dec 2021 10:51:14: 21000000 INFO @ Fri, 10 Dec 2021 10:51:16: 14000000 INFO @ Fri, 10 Dec 2021 10:51:19: 15000000 INFO @ Fri, 10 Dec 2021 10:51:23: 22000000 INFO @ Fri, 10 Dec 2021 10:51:25: 15000000 INFO @ Fri, 10 Dec 2021 10:51:30: 16000000 INFO @ Fri, 10 Dec 2021 10:51:33: 23000000 INFO @ Fri, 10 Dec 2021 10:51:35: 16000000 INFO @ Fri, 10 Dec 2021 10:51:41: 17000000 INFO @ Fri, 10 Dec 2021 10:51:43: 24000000 INFO @ Fri, 10 Dec 2021 10:51:45: 17000000 INFO @ Fri, 10 Dec 2021 10:51:52: 18000000 INFO @ Fri, 10 Dec 2021 10:51:53: 25000000 INFO @ Fri, 10 Dec 2021 10:51:55: 18000000 INFO @ Fri, 10 Dec 2021 10:52:03: 26000000 INFO @ Fri, 10 Dec 2021 10:52:03: 19000000 INFO @ Fri, 10 Dec 2021 10:52:05: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:52:12: 27000000 INFO @ Fri, 10 Dec 2021 10:52:14: 20000000 INFO @ Fri, 10 Dec 2021 10:52:15: 20000000 INFO @ Fri, 10 Dec 2021 10:52:22: 28000000 INFO @ Fri, 10 Dec 2021 10:52:25: 21000000 INFO @ Fri, 10 Dec 2021 10:52:26: 21000000 INFO @ Fri, 10 Dec 2021 10:52:31: 29000000 INFO @ Fri, 10 Dec 2021 10:52:36: 22000000 INFO @ Fri, 10 Dec 2021 10:52:37: 22000000 INFO @ Fri, 10 Dec 2021 10:52:40: 30000000 INFO @ Fri, 10 Dec 2021 10:52:47: 23000000 INFO @ Fri, 10 Dec 2021 10:52:48: 23000000 INFO @ Fri, 10 Dec 2021 10:52:50: 31000000 INFO @ Fri, 10 Dec 2021 10:52:59: 24000000 INFO @ Fri, 10 Dec 2021 10:52:59: 32000000 INFO @ Fri, 10 Dec 2021 10:53:00: 24000000 INFO @ Fri, 10 Dec 2021 10:53:08: 33000000 INFO @ Fri, 10 Dec 2021 10:53:10: 25000000 INFO @ Fri, 10 Dec 2021 10:53:11: 25000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:53:18: 34000000 INFO @ Fri, 10 Dec 2021 10:53:21: 26000000 INFO @ Fri, 10 Dec 2021 10:53:22: 26000000 INFO @ Fri, 10 Dec 2021 10:53:27: 35000000 INFO @ Fri, 10 Dec 2021 10:53:32: 27000000 INFO @ Fri, 10 Dec 2021 10:53:33: 27000000 INFO @ Fri, 10 Dec 2021 10:53:36: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 10:53:36: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 10:53:36: #1 total tags in treatment: 14983736 INFO @ Fri, 10 Dec 2021 10:53:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:53:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:53:36: #1 tags after filtering in treatment: 13725694 INFO @ Fri, 10 Dec 2021 10:53:36: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 10:53:36: #1 finished! INFO @ Fri, 10 Dec 2021 10:53:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:53:37: #2 number of paired peaks: 792 WARNING @ Fri, 10 Dec 2021 10:53:37: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Fri, 10 Dec 2021 10:53:37: start model_add_line... INFO @ Fri, 10 Dec 2021 10:53:37: start X-correlation... INFO @ Fri, 10 Dec 2021 10:53:37: end of X-cor INFO @ Fri, 10 Dec 2021 10:53:37: #2 finished! INFO @ Fri, 10 Dec 2021 10:53:37: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 10:53:37: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 10:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.05_model.r WARNING @ Fri, 10 Dec 2021 10:53:37: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:53:37: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Fri, 10 Dec 2021 10:53:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 10:53:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:53:43: 28000000 INFO @ Fri, 10 Dec 2021 10:53:44: 28000000 INFO @ Fri, 10 Dec 2021 10:53:53: 29000000 INFO @ Fri, 10 Dec 2021 10:53:54: 29000000 INFO @ Fri, 10 Dec 2021 10:54:04: 30000000 INFO @ Fri, 10 Dec 2021 10:54:05: 30000000 INFO @ Fri, 10 Dec 2021 10:54:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:54:15: 31000000 INFO @ Fri, 10 Dec 2021 10:54:15: 31000000 INFO @ Fri, 10 Dec 2021 10:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.05_summits.bed INFO @ Fri, 10 Dec 2021 10:54:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3041 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:54:25: 32000000 INFO @ Fri, 10 Dec 2021 10:54:26: 32000000 INFO @ Fri, 10 Dec 2021 10:54:36: 33000000 INFO @ Fri, 10 Dec 2021 10:54:37: 33000000 INFO @ Fri, 10 Dec 2021 10:54:47: 34000000 INFO @ Fri, 10 Dec 2021 10:54:47: 34000000 INFO @ Fri, 10 Dec 2021 10:54:57: 35000000 INFO @ Fri, 10 Dec 2021 10:54:58: 35000000 INFO @ Fri, 10 Dec 2021 10:55:07: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 10:55:07: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 10:55:07: #1 total tags in treatment: 14983736 INFO @ Fri, 10 Dec 2021 10:55:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:55:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:55:07: #1 tags after filtering in treatment: 13725694 INFO @ Fri, 10 Dec 2021 10:55:07: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 10:55:07: #1 finished! INFO @ Fri, 10 Dec 2021 10:55:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:55:08: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 10:55:08: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 10:55:08: #1 total tags in treatment: 14983736 INFO @ Fri, 10 Dec 2021 10:55:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:55:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:55:08: #1 tags after filtering in treatment: 13725694 INFO @ Fri, 10 Dec 2021 10:55:08: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 10:55:08: #1 finished! INFO @ Fri, 10 Dec 2021 10:55:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:55:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:55:08: #2 number of paired peaks: 792 WARNING @ Fri, 10 Dec 2021 10:55:08: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Fri, 10 Dec 2021 10:55:08: start model_add_line... INFO @ Fri, 10 Dec 2021 10:55:08: start X-correlation... INFO @ Fri, 10 Dec 2021 10:55:08: end of X-cor INFO @ Fri, 10 Dec 2021 10:55:08: #2 finished! INFO @ Fri, 10 Dec 2021 10:55:08: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 10:55:08: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 10:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.10_model.r WARNING @ Fri, 10 Dec 2021 10:55:08: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:55:08: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Fri, 10 Dec 2021 10:55:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 10:55:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:55:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:55:09: #2 number of paired peaks: 792 WARNING @ Fri, 10 Dec 2021 10:55:09: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Fri, 10 Dec 2021 10:55:09: start model_add_line... INFO @ Fri, 10 Dec 2021 10:55:09: start X-correlation... INFO @ Fri, 10 Dec 2021 10:55:09: end of X-cor INFO @ Fri, 10 Dec 2021 10:55:09: #2 finished! INFO @ Fri, 10 Dec 2021 10:55:09: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 10:55:09: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 10:55:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.20_model.r WARNING @ Fri, 10 Dec 2021 10:55:09: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:55:09: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Fri, 10 Dec 2021 10:55:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 10:55:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:55:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:55:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:55:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:55:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:55:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:55:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.10_summits.bed INFO @ Fri, 10 Dec 2021 10:55:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1962 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8694697/SRX8694697.20_summits.bed INFO @ Fri, 10 Dec 2021 10:55:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1102 records, 4 fields): 8 millis CompletedMACS2peakCalling