Job ID = 14170258 SRX = SRX8556386 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22829958 spots for SRR12024942/SRR12024942.sra Written 22829958 spots for SRR12024942/SRR12024942.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170868 ("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: 00:58:26 22829958 reads; of these: 22829958 (100.00%) were paired; of these: 15828658 (69.33%) aligned concordantly 0 times 4496956 (19.70%) aligned concordantly exactly 1 time 2504344 (10.97%) aligned concordantly >1 times ---- 15828658 pairs aligned concordantly 0 times; of these: 841724 (5.32%) aligned discordantly 1 time ---- 14986934 pairs aligned 0 times concordantly or discordantly; of these: 29973868 mates make up the pairs; of these: 27073756 (90.32%) aligned 0 times 753780 (2.51%) aligned exactly 1 time 2146332 (7.16%) aligned >1 times 40.71% overall alignment rate Time searching: 00:58:26 Overall time: 00:58:26 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 16 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] 3718033 / 7740859 = 0.4803 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 07:03:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.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 07:03:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:03:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:04:03: 1000000 INFO @ Sat, 11 Dec 2021 07:04:11: 2000000 INFO @ Sat, 11 Dec 2021 07:04:18: 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 @ Sat, 11 Dec 2021 07:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.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 07:04:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:04:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:04:25: 4000000 INFO @ Sat, 11 Dec 2021 07:04:34: 1000000 INFO @ Sat, 11 Dec 2021 07:04:34: 5000000 INFO @ Sat, 11 Dec 2021 07:04:42: 2000000 INFO @ Sat, 11 Dec 2021 07:04:42: 6000000 INFO @ Sat, 11 Dec 2021 07:04:50: 3000000 INFO @ Sat, 11 Dec 2021 07:04:51: 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 07:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.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 07:04:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:04:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:04:59: 4000000 INFO @ Sat, 11 Dec 2021 07:05:00: 8000000 INFO @ Sat, 11 Dec 2021 07:05:03: 1000000 INFO @ Sat, 11 Dec 2021 07:05:07: 5000000 INFO @ Sat, 11 Dec 2021 07:05:09: 9000000 INFO @ Sat, 11 Dec 2021 07:05:10: 2000000 INFO @ Sat, 11 Dec 2021 07:05:16: 6000000 INFO @ Sat, 11 Dec 2021 07:05:18: 10000000 INFO @ Sat, 11 Dec 2021 07:05:18: 3000000 INFO @ Sat, 11 Dec 2021 07:05:24: 7000000 INFO @ Sat, 11 Dec 2021 07:05:25: 4000000 INFO @ Sat, 11 Dec 2021 07:05:26: 11000000 INFO @ Sat, 11 Dec 2021 07:05:27: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:05:27: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:05:27: #1 total tags in treatment: 3553605 INFO @ Sat, 11 Dec 2021 07:05:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:05:27: #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 07:05:28: #1 tags after filtering in treatment: 2908063 INFO @ Sat, 11 Dec 2021 07:05:28: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 07:05:28: #1 finished! INFO @ Sat, 11 Dec 2021 07:05:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:05:28: #2 number of paired peaks: 1811 INFO @ Sat, 11 Dec 2021 07:05:28: start model_add_line... INFO @ Sat, 11 Dec 2021 07:05:28: start X-correlation... INFO @ Sat, 11 Dec 2021 07:05:28: end of X-cor INFO @ Sat, 11 Dec 2021 07:05:28: #2 finished! INFO @ Sat, 11 Dec 2021 07:05:28: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:05:28: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:05:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.05_model.r WARNING @ Sat, 11 Dec 2021 07:05:28: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:05:28: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:05:28: #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 07:05:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:05:32: 8000000 INFO @ Sat, 11 Dec 2021 07:05:33: 5000000 INFO @ Sat, 11 Dec 2021 07:05:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:05:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:05:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:05:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.05_summits.bed INFO @ Sat, 11 Dec 2021 07:05:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7601 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:05:40: 9000000 INFO @ Sat, 11 Dec 2021 07:05:40: 6000000 INFO @ Sat, 11 Dec 2021 07:05:48: 7000000 INFO @ Sat, 11 Dec 2021 07:05:48: 10000000 INFO @ Sat, 11 Dec 2021 07:05:55: 8000000 INFO @ Sat, 11 Dec 2021 07:05:55: 11000000 INFO @ Sat, 11 Dec 2021 07:05:57: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:05:57: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:05:57: #1 total tags in treatment: 3553605 INFO @ Sat, 11 Dec 2021 07:05:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:05:57: #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 07:05:57: #1 tags after filtering in treatment: 2908063 INFO @ Sat, 11 Dec 2021 07:05:57: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 07:05:57: #1 finished! INFO @ Sat, 11 Dec 2021 07:05:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:05:57: #2 number of paired peaks: 1811 INFO @ Sat, 11 Dec 2021 07:05:57: start model_add_line... INFO @ Sat, 11 Dec 2021 07:05:57: start X-correlation... INFO @ Sat, 11 Dec 2021 07:05:57: end of X-cor INFO @ Sat, 11 Dec 2021 07:05:57: #2 finished! INFO @ Sat, 11 Dec 2021 07:05:57: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:05:57: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.10_model.r WARNING @ Sat, 11 Dec 2021 07:05:57: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:05:57: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:05:57: #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 07:05:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:06:03: 9000000 INFO @ Sat, 11 Dec 2021 07:06:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:06:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:06:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:06:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.10_summits.bed INFO @ Sat, 11 Dec 2021 07:06:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2579 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:06:11: 10000000 INFO @ Sat, 11 Dec 2021 07:06:18: 11000000 INFO @ Sat, 11 Dec 2021 07:06:19: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:06:19: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:06:19: #1 total tags in treatment: 3553605 INFO @ Sat, 11 Dec 2021 07:06:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:06:19: #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 07:06:19: #1 tags after filtering in treatment: 2908063 INFO @ Sat, 11 Dec 2021 07:06:19: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 11 Dec 2021 07:06:19: #1 finished! INFO @ Sat, 11 Dec 2021 07:06:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:06:19: #2 number of paired peaks: 1811 INFO @ Sat, 11 Dec 2021 07:06:19: start model_add_line... INFO @ Sat, 11 Dec 2021 07:06:20: start X-correlation... INFO @ Sat, 11 Dec 2021 07:06:20: end of X-cor INFO @ Sat, 11 Dec 2021 07:06:20: #2 finished! INFO @ Sat, 11 Dec 2021 07:06:20: #2 predicted fragment length is 185 bps INFO @ Sat, 11 Dec 2021 07:06:20: #2 alternative fragment length(s) may be 185 bps INFO @ Sat, 11 Dec 2021 07:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.20_model.r WARNING @ Sat, 11 Dec 2021 07:06:20: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:06:20: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Sat, 11 Dec 2021 07:06:20: #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 07:06:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:06:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:06:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:06:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:06:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:06:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556386/SRX8556386.20_summits.bed INFO @ Sat, 11 Dec 2021 07:06:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1193 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。