Job ID = 14168694 SRX = ERX3978760 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22372304 spots for ERR3975775/ERR3975775.sra Written 22372304 spots for ERR3975775/ERR3975775.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169848 ("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: 00:56:58 22372304 reads; of these: 22372304 (100.00%) were paired; of these: 9376659 (41.91%) aligned concordantly 0 times 8405144 (37.57%) aligned concordantly exactly 1 time 4590501 (20.52%) aligned concordantly >1 times ---- 9376659 pairs aligned concordantly 0 times; of these: 2868714 (30.59%) aligned discordantly 1 time ---- 6507945 pairs aligned 0 times concordantly or discordantly; of these: 13015890 mates make up the pairs; of these: 8905545 (68.42%) aligned 0 times 463583 (3.56%) aligned exactly 1 time 3646762 (28.02%) aligned >1 times 80.10% overall alignment rate Time searching: 00:56:58 Overall time: 00:56:58 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 24 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] 3496045 / 15770680 = 0.2217 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 20:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.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 20:35:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:35:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:35:34: 1000000 INFO @ Fri, 10 Dec 2021 20:35:40: 2000000 INFO @ Fri, 10 Dec 2021 20:35:46: 3000000 INFO @ Fri, 10 Dec 2021 20:35:52: 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 @ Fri, 10 Dec 2021 20:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.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 20:35:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:35:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:35:58: 5000000 INFO @ Fri, 10 Dec 2021 20:36:04: 1000000 INFO @ Fri, 10 Dec 2021 20:36:05: 6000000 INFO @ Fri, 10 Dec 2021 20:36:10: 2000000 INFO @ Fri, 10 Dec 2021 20:36:11: 7000000 INFO @ Fri, 10 Dec 2021 20:36:17: 3000000 INFO @ Fri, 10 Dec 2021 20:36:17: 8000000 INFO @ Fri, 10 Dec 2021 20:36:23: 4000000 INFO @ Fri, 10 Dec 2021 20:36:23: 9000000 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 20:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.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 20:36:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:36:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:36:29: 5000000 INFO @ Fri, 10 Dec 2021 20:36:29: 10000000 INFO @ Fri, 10 Dec 2021 20:36:34: 1000000 INFO @ Fri, 10 Dec 2021 20:36:35: 6000000 INFO @ Fri, 10 Dec 2021 20:36:35: 11000000 INFO @ Fri, 10 Dec 2021 20:36:40: 2000000 INFO @ Fri, 10 Dec 2021 20:36:42: 12000000 INFO @ Fri, 10 Dec 2021 20:36:42: 7000000 INFO @ Fri, 10 Dec 2021 20:36:46: 3000000 INFO @ Fri, 10 Dec 2021 20:36:48: 13000000 INFO @ Fri, 10 Dec 2021 20:36:48: 8000000 INFO @ Fri, 10 Dec 2021 20:36:53: 4000000 INFO @ Fri, 10 Dec 2021 20:36:54: 14000000 INFO @ Fri, 10 Dec 2021 20:36:55: 9000000 INFO @ Fri, 10 Dec 2021 20:36:59: 5000000 INFO @ Fri, 10 Dec 2021 20:37:01: 15000000 INFO @ Fri, 10 Dec 2021 20:37:01: 10000000 INFO @ Fri, 10 Dec 2021 20:37:05: 6000000 INFO @ Fri, 10 Dec 2021 20:37:07: 16000000 INFO @ Fri, 10 Dec 2021 20:37:07: 11000000 INFO @ Fri, 10 Dec 2021 20:37:12: 7000000 INFO @ Fri, 10 Dec 2021 20:37:13: 17000000 INFO @ Fri, 10 Dec 2021 20:37:13: 12000000 INFO @ Fri, 10 Dec 2021 20:37:18: 8000000 INFO @ Fri, 10 Dec 2021 20:37:19: 18000000 INFO @ Fri, 10 Dec 2021 20:37:20: 13000000 INFO @ Fri, 10 Dec 2021 20:37:24: 9000000 INFO @ Fri, 10 Dec 2021 20:37:26: 19000000 INFO @ Fri, 10 Dec 2021 20:37:26: 14000000 INFO @ Fri, 10 Dec 2021 20:37:31: 10000000 INFO @ Fri, 10 Dec 2021 20:37:31: 20000000 INFO @ Fri, 10 Dec 2021 20:37:32: 15000000 INFO @ Fri, 10 Dec 2021 20:37:37: 21000000 INFO @ Fri, 10 Dec 2021 20:37:37: 11000000 INFO @ Fri, 10 Dec 2021 20:37:38: 16000000 INFO @ Fri, 10 Dec 2021 20:37:43: 22000000 INFO @ Fri, 10 Dec 2021 20:37:44: 12000000 INFO @ Fri, 10 Dec 2021 20:37:45: 17000000 INFO @ Fri, 10 Dec 2021 20:37:49: 23000000 INFO @ Fri, 10 Dec 2021 20:37:50: 13000000 INFO @ Fri, 10 Dec 2021 20:37:51: 18000000 INFO @ Fri, 10 Dec 2021 20:37:55: 24000000 INFO @ Fri, 10 Dec 2021 20:37:56: 14000000 INFO @ Fri, 10 Dec 2021 20:37:57: 19000000 INFO @ Fri, 10 Dec 2021 20:38:01: 25000000 INFO @ Fri, 10 Dec 2021 20:38:02: 15000000 INFO @ Fri, 10 Dec 2021 20:38:03: 20000000 INFO @ Fri, 10 Dec 2021 20:38:08: 26000000 INFO @ Fri, 10 Dec 2021 20:38:08: 21000000 INFO @ Fri, 10 Dec 2021 20:38:08: 16000000 INFO @ Fri, 10 Dec 2021 20:38:14: 22000000 INFO @ Fri, 10 Dec 2021 20:38:14: 27000000 INFO @ Fri, 10 Dec 2021 20:38:15: 17000000 INFO @ Fri, 10 Dec 2021 20:38:20: 23000000 INFO @ Fri, 10 Dec 2021 20:38:20: 28000000 INFO @ Fri, 10 Dec 2021 20:38:21: 18000000 INFO @ Fri, 10 Dec 2021 20:38:26: 24000000 INFO @ Fri, 10 Dec 2021 20:38:26: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:38:26: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:38:26: #1 total tags in treatment: 9689567 INFO @ Fri, 10 Dec 2021 20:38:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:38:26: #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 20:38:27: #1 tags after filtering in treatment: 7086874 INFO @ Fri, 10 Dec 2021 20:38:27: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 20:38:27: #1 finished! INFO @ Fri, 10 Dec 2021 20:38:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:38:27: 19000000 INFO @ Fri, 10 Dec 2021 20:38:27: #2 number of paired peaks: 4296 INFO @ Fri, 10 Dec 2021 20:38:27: start model_add_line... INFO @ Fri, 10 Dec 2021 20:38:27: start X-correlation... INFO @ Fri, 10 Dec 2021 20:38:27: end of X-cor INFO @ Fri, 10 Dec 2021 20:38:27: #2 finished! INFO @ Fri, 10 Dec 2021 20:38:27: #2 predicted fragment length is 202 bps INFO @ Fri, 10 Dec 2021 20:38:27: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 10 Dec 2021 20:38:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.05_model.r WARNING @ Fri, 10 Dec 2021 20:38:27: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:38:27: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Fri, 10 Dec 2021 20:38:27: #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 20:38:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:38:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:38:32: 25000000 INFO @ Fri, 10 Dec 2021 20:38:33: 20000000 INFO @ Fri, 10 Dec 2021 20:38:39: 21000000 INFO @ Fri, 10 Dec 2021 20:38:39: 26000000 INFO @ Fri, 10 Dec 2021 20:38:44: 22000000 INFO @ Fri, 10 Dec 2021 20:38:45: 27000000 INFO @ Fri, 10 Dec 2021 20:38:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:38:50: 23000000 INFO @ Fri, 10 Dec 2021 20:38:51: 28000000 INFO @ Fri, 10 Dec 2021 20:38:56: 24000000 INFO @ Fri, 10 Dec 2021 20:38:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:38:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:38:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.05_summits.bed INFO @ Fri, 10 Dec 2021 20:38:57: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:38:57: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:38:57: #1 total tags in treatment: 9689567 INFO @ Fri, 10 Dec 2021 20:38:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:38:57: #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 20:38:57: Done! INFO @ Fri, 10 Dec 2021 20:38:57: #1 tags after filtering in treatment: 7086874 INFO @ Fri, 10 Dec 2021 20:38:57: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 20:38:57: #1 finished! INFO @ Fri, 10 Dec 2021 20:38:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:38:57: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10422 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:38:58: #2 number of paired peaks: 4296 INFO @ Fri, 10 Dec 2021 20:38:58: start model_add_line... INFO @ Fri, 10 Dec 2021 20:38:58: start X-correlation... INFO @ Fri, 10 Dec 2021 20:38:58: end of X-cor INFO @ Fri, 10 Dec 2021 20:38:58: #2 finished! INFO @ Fri, 10 Dec 2021 20:38:58: #2 predicted fragment length is 202 bps INFO @ Fri, 10 Dec 2021 20:38:58: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 10 Dec 2021 20:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.10_model.r WARNING @ Fri, 10 Dec 2021 20:38:58: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:38:58: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Fri, 10 Dec 2021 20:38:58: #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 20:38:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:38:58: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:39:02: 25000000 INFO @ Fri, 10 Dec 2021 20:39:09: 26000000 INFO @ Fri, 10 Dec 2021 20:39:15: 27000000 INFO @ Fri, 10 Dec 2021 20:39:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:39:21: 28000000 INFO @ Fri, 10 Dec 2021 20:39:27: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:39:27: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:39:27: #1 total tags in treatment: 9689567 INFO @ Fri, 10 Dec 2021 20:39:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:39:27: #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 20:39:27: #1 tags after filtering in treatment: 7086874 INFO @ Fri, 10 Dec 2021 20:39:27: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 20:39:27: #1 finished! INFO @ Fri, 10 Dec 2021 20:39:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:39:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:39:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:39:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:39:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.10_summits.bed INFO @ Fri, 10 Dec 2021 20:39:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6675 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:39:28: #2 number of paired peaks: 4296 INFO @ Fri, 10 Dec 2021 20:39:28: start model_add_line... INFO @ Fri, 10 Dec 2021 20:39:28: start X-correlation... INFO @ Fri, 10 Dec 2021 20:39:28: end of X-cor INFO @ Fri, 10 Dec 2021 20:39:28: #2 finished! INFO @ Fri, 10 Dec 2021 20:39:28: #2 predicted fragment length is 202 bps INFO @ Fri, 10 Dec 2021 20:39:28: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 10 Dec 2021 20:39:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.20_model.r WARNING @ Fri, 10 Dec 2021 20:39:28: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:39:28: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Fri, 10 Dec 2021 20:39:28: #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 20:39:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:39:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:39:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:39:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978760/ERX3978760.20_summits.bed INFO @ Fri, 10 Dec 2021 20:39:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2894 records, 4 fields): 4 millis CompletedMACS2peakCalling