Job ID = 14168653 SRX = ERX3978758 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18688166 spots for ERR3975772/ERR3975772.sra Written 18688166 spots for ERR3975772/ERR3975772.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169804 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:42:51 18688166 reads; of these: 18688166 (100.00%) were paired; of these: 5395266 (28.87%) aligned concordantly 0 times 10734764 (57.44%) aligned concordantly exactly 1 time 2558136 (13.69%) aligned concordantly >1 times ---- 5395266 pairs aligned concordantly 0 times; of these: 2809415 (52.07%) aligned discordantly 1 time ---- 2585851 pairs aligned 0 times concordantly or discordantly; of these: 5171702 mates make up the pairs; of these: 3537961 (68.41%) aligned 0 times 410530 (7.94%) aligned exactly 1 time 1223211 (23.65%) aligned >1 times 90.53% overall alignment rate Time searching: 00:42:52 Overall time: 00:42:52 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] 2055400 / 16041495 = 0.1281 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 20:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.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 20:06:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:06:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:06:46: 1000000 INFO @ Fri, 10 Dec 2021 20:06:52: 2000000 INFO @ Fri, 10 Dec 2021 20:06:59: 3000000 INFO @ Fri, 10 Dec 2021 20:07:05: 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 20:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.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 20:07:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:07:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:07:12: 5000000 INFO @ Fri, 10 Dec 2021 20:07:16: 1000000 INFO @ Fri, 10 Dec 2021 20:07:19: 6000000 INFO @ Fri, 10 Dec 2021 20:07:23: 2000000 INFO @ Fri, 10 Dec 2021 20:07:26: 7000000 INFO @ Fri, 10 Dec 2021 20:07:30: 3000000 INFO @ Fri, 10 Dec 2021 20:07:32: 8000000 INFO @ Fri, 10 Dec 2021 20:07:36: 4000000 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 20:07:39: 9000000 INFO @ Fri, 10 Dec 2021 20:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.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 20:07:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:07:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:07:43: 5000000 INFO @ Fri, 10 Dec 2021 20:07:46: 10000000 INFO @ Fri, 10 Dec 2021 20:07:46: 1000000 INFO @ Fri, 10 Dec 2021 20:07:50: 6000000 INFO @ Fri, 10 Dec 2021 20:07:52: 11000000 INFO @ Fri, 10 Dec 2021 20:07:53: 2000000 INFO @ Fri, 10 Dec 2021 20:07:56: 7000000 INFO @ Fri, 10 Dec 2021 20:07:59: 12000000 INFO @ Fri, 10 Dec 2021 20:07:59: 3000000 INFO @ Fri, 10 Dec 2021 20:08:03: 8000000 INFO @ Fri, 10 Dec 2021 20:08:06: 13000000 INFO @ Fri, 10 Dec 2021 20:08:06: 4000000 INFO @ Fri, 10 Dec 2021 20:08:10: 9000000 INFO @ Fri, 10 Dec 2021 20:08:13: 14000000 INFO @ Fri, 10 Dec 2021 20:08:13: 5000000 INFO @ Fri, 10 Dec 2021 20:08:17: 10000000 INFO @ Fri, 10 Dec 2021 20:08:20: 6000000 INFO @ Fri, 10 Dec 2021 20:08:20: 15000000 INFO @ Fri, 10 Dec 2021 20:08:24: 11000000 INFO @ Fri, 10 Dec 2021 20:08:26: 7000000 INFO @ Fri, 10 Dec 2021 20:08:26: 16000000 INFO @ Fri, 10 Dec 2021 20:08:30: 12000000 INFO @ Fri, 10 Dec 2021 20:08:33: 8000000 INFO @ Fri, 10 Dec 2021 20:08:33: 17000000 INFO @ Fri, 10 Dec 2021 20:08:37: 13000000 INFO @ Fri, 10 Dec 2021 20:08:40: 9000000 INFO @ Fri, 10 Dec 2021 20:08:40: 18000000 INFO @ Fri, 10 Dec 2021 20:08:44: 14000000 INFO @ Fri, 10 Dec 2021 20:08:46: 10000000 INFO @ Fri, 10 Dec 2021 20:08:47: 19000000 INFO @ Fri, 10 Dec 2021 20:08:51: 15000000 INFO @ Fri, 10 Dec 2021 20:08:53: 11000000 INFO @ Fri, 10 Dec 2021 20:08:53: 20000000 INFO @ Fri, 10 Dec 2021 20:08:57: 16000000 INFO @ Fri, 10 Dec 2021 20:09:00: 12000000 INFO @ Fri, 10 Dec 2021 20:09:00: 21000000 INFO @ Fri, 10 Dec 2021 20:09:04: 17000000 INFO @ Fri, 10 Dec 2021 20:09:06: 13000000 INFO @ Fri, 10 Dec 2021 20:09:07: 22000000 INFO @ Fri, 10 Dec 2021 20:09:10: 18000000 INFO @ Fri, 10 Dec 2021 20:09:13: 14000000 INFO @ Fri, 10 Dec 2021 20:09:13: 23000000 INFO @ Fri, 10 Dec 2021 20:09:17: 19000000 INFO @ Fri, 10 Dec 2021 20:09:19: 15000000 INFO @ Fri, 10 Dec 2021 20:09:19: 24000000 INFO @ Fri, 10 Dec 2021 20:09:24: 20000000 INFO @ Fri, 10 Dec 2021 20:09:26: 16000000 INFO @ Fri, 10 Dec 2021 20:09:26: 25000000 INFO @ Fri, 10 Dec 2021 20:09:31: 21000000 INFO @ Fri, 10 Dec 2021 20:09:33: 17000000 INFO @ Fri, 10 Dec 2021 20:09:33: 26000000 INFO @ Fri, 10 Dec 2021 20:09:38: 22000000 INFO @ Fri, 10 Dec 2021 20:09:40: 18000000 INFO @ Fri, 10 Dec 2021 20:09:40: 27000000 INFO @ Fri, 10 Dec 2021 20:09:44: 23000000 INFO @ Fri, 10 Dec 2021 20:09:46: 19000000 INFO @ Fri, 10 Dec 2021 20:09:47: 28000000 INFO @ Fri, 10 Dec 2021 20:09:51: 24000000 INFO @ Fri, 10 Dec 2021 20:09:53: 20000000 INFO @ Fri, 10 Dec 2021 20:09:54: 29000000 INFO @ Fri, 10 Dec 2021 20:09:57: 25000000 INFO @ Fri, 10 Dec 2021 20:09:59: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:09:59: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:09:59: #1 total tags in treatment: 11365231 INFO @ Fri, 10 Dec 2021 20:09:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:09:59: #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 20:09:59: #1 tags after filtering in treatment: 8510755 INFO @ Fri, 10 Dec 2021 20:09:59: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 20:09:59: #1 finished! INFO @ Fri, 10 Dec 2021 20:09:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:10:00: 21000000 INFO @ Fri, 10 Dec 2021 20:10:00: #2 number of paired peaks: 2977 INFO @ Fri, 10 Dec 2021 20:10:00: start model_add_line... INFO @ Fri, 10 Dec 2021 20:10:00: start X-correlation... INFO @ Fri, 10 Dec 2021 20:10:00: end of X-cor INFO @ Fri, 10 Dec 2021 20:10:00: #2 finished! INFO @ Fri, 10 Dec 2021 20:10:00: #2 predicted fragment length is 206 bps INFO @ Fri, 10 Dec 2021 20:10:00: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 10 Dec 2021 20:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.05_model.r WARNING @ Fri, 10 Dec 2021 20:10:00: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:10:00: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Fri, 10 Dec 2021 20:10:00: #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 20:10:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:10:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:10:04: 26000000 INFO @ Fri, 10 Dec 2021 20:10:06: 22000000 INFO @ Fri, 10 Dec 2021 20:10:11: 27000000 INFO @ Fri, 10 Dec 2021 20:10:13: 23000000 INFO @ Fri, 10 Dec 2021 20:10:18: 28000000 INFO @ Fri, 10 Dec 2021 20:10:19: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:10:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:10:24: 29000000 INFO @ Fri, 10 Dec 2021 20:10:26: 25000000 INFO @ Fri, 10 Dec 2021 20:10:29: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:10:29: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:10:29: #1 total tags in treatment: 11365231 INFO @ Fri, 10 Dec 2021 20:10:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:10:29: #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 20:10:29: #1 tags after filtering in treatment: 8510755 INFO @ Fri, 10 Dec 2021 20:10:29: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 20:10:29: #1 finished! INFO @ Fri, 10 Dec 2021 20:10:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:10:30: #2 number of paired peaks: 2977 INFO @ Fri, 10 Dec 2021 20:10:30: start model_add_line... INFO @ Fri, 10 Dec 2021 20:10:30: start X-correlation... INFO @ Fri, 10 Dec 2021 20:10:30: end of X-cor INFO @ Fri, 10 Dec 2021 20:10:30: #2 finished! INFO @ Fri, 10 Dec 2021 20:10:30: #2 predicted fragment length is 206 bps INFO @ Fri, 10 Dec 2021 20:10:30: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 10 Dec 2021 20:10:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.10_model.r WARNING @ Fri, 10 Dec 2021 20:10:30: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:10:30: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Fri, 10 Dec 2021 20:10:30: #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 20:10:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:10:32: 26000000 INFO @ Fri, 10 Dec 2021 20:10:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.05_summits.bed INFO @ Fri, 10 Dec 2021 20:10:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11225 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:10:39: 27000000 INFO @ Fri, 10 Dec 2021 20:10:45: 28000000 INFO @ Fri, 10 Dec 2021 20:10:52: 29000000 INFO @ Fri, 10 Dec 2021 20:10:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:10:57: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:10:57: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:10:57: #1 total tags in treatment: 11365231 INFO @ Fri, 10 Dec 2021 20:10:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:10:57: #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 20:10:57: #1 tags after filtering in treatment: 8510755 INFO @ Fri, 10 Dec 2021 20:10:57: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 20:10:57: #1 finished! INFO @ Fri, 10 Dec 2021 20:10:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:10:58: #2 number of paired peaks: 2977 INFO @ Fri, 10 Dec 2021 20:10:58: start model_add_line... INFO @ Fri, 10 Dec 2021 20:10:58: start X-correlation... INFO @ Fri, 10 Dec 2021 20:10:58: end of X-cor INFO @ Fri, 10 Dec 2021 20:10:58: #2 finished! INFO @ Fri, 10 Dec 2021 20:10:58: #2 predicted fragment length is 206 bps INFO @ Fri, 10 Dec 2021 20:10:58: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 10 Dec 2021 20:10:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.20_model.r WARNING @ Fri, 10 Dec 2021 20:10:58: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:10:58: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Fri, 10 Dec 2021 20:10:58: #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 20:10:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:10:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:11:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:11:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:11:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.10_summits.bed INFO @ Fri, 10 Dec 2021 20:11:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6880 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:11:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:11:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:11:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:11:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978758/ERX3978758.20_summits.bed INFO @ Fri, 10 Dec 2021 20:11:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2815 records, 4 fields): 4 millis CompletedMACS2peakCalling