Job ID = 14172108 SRX = SRX9103813 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T05:16:51 fastq-dump.2.10.7 err: data corrupt while executing function within transform module - failed SRR12621013/SRR12621013.sra ============================================================= An error occurred during processing. A report was generated into the file '/home/okishinya/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to 'sra-tools@ncbi.nlm.nih.gov' for assistance. ============================================================= fastq-dump quit with error code 3 fastq に変換しました。 bowtie でマッピング中... Your job 14172602 ("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: 00:16:50 19972096 reads; of these: 19972096 (100.00%) were paired; of these: 7979380 (39.95%) aligned concordantly 0 times 7440230 (37.25%) aligned concordantly exactly 1 time 4552486 (22.79%) aligned concordantly >1 times ---- 7979380 pairs aligned concordantly 0 times; of these: 1177439 (14.76%) aligned discordantly 1 time ---- 6801941 pairs aligned 0 times concordantly or discordantly; of these: 13603882 mates make up the pairs; of these: 12282807 (90.29%) aligned 0 times 437506 (3.22%) aligned exactly 1 time 883569 (6.49%) aligned >1 times 69.25% overall alignment rate Time searching: 00:16:50 Overall time: 00:16:50 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_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] 3064513 / 13028234 = 0.2352 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 14:40:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.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 14:40:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:40:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:40:43: 1000000 INFO @ Sat, 11 Dec 2021 14:40:48: 2000000 INFO @ Sat, 11 Dec 2021 14:40:52: 3000000 INFO @ Sat, 11 Dec 2021 14:40:57: 4000000 INFO @ Sat, 11 Dec 2021 14:41:01: 5000000 INFO @ Sat, 11 Dec 2021 14:41:06: 6000000 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 14:41:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.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 14:41:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:41:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:41:11: 7000000 INFO @ Sat, 11 Dec 2021 14:41:13: 1000000 INFO @ Sat, 11 Dec 2021 14:41:16: 8000000 INFO @ Sat, 11 Dec 2021 14:41:18: 2000000 INFO @ Sat, 11 Dec 2021 14:41:21: 9000000 INFO @ Sat, 11 Dec 2021 14:41:23: 3000000 INFO @ Sat, 11 Dec 2021 14:41:25: 10000000 INFO @ Sat, 11 Dec 2021 14:41:28: 4000000 INFO @ Sat, 11 Dec 2021 14:41:30: 11000000 INFO @ Sat, 11 Dec 2021 14:41:33: 5000000 INFO @ Sat, 11 Dec 2021 14:41:35: 12000000 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 14:41:38: 6000000 INFO @ Sat, 11 Dec 2021 14:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.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 14:41:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:41:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:41:40: 13000000 INFO @ Sat, 11 Dec 2021 14:41:43: 7000000 INFO @ Sat, 11 Dec 2021 14:41:44: 1000000 INFO @ Sat, 11 Dec 2021 14:41:45: 14000000 INFO @ Sat, 11 Dec 2021 14:41:48: 8000000 INFO @ Sat, 11 Dec 2021 14:41:50: 2000000 INFO @ Sat, 11 Dec 2021 14:41:50: 15000000 INFO @ Sat, 11 Dec 2021 14:41:53: 9000000 INFO @ Sat, 11 Dec 2021 14:41:55: 16000000 INFO @ Sat, 11 Dec 2021 14:41:56: 3000000 INFO @ Sat, 11 Dec 2021 14:41:58: 10000000 INFO @ Sat, 11 Dec 2021 14:42:00: 17000000 INFO @ Sat, 11 Dec 2021 14:42:02: 4000000 INFO @ Sat, 11 Dec 2021 14:42:03: 11000000 INFO @ Sat, 11 Dec 2021 14:42:05: 18000000 INFO @ Sat, 11 Dec 2021 14:42:08: 5000000 INFO @ Sat, 11 Dec 2021 14:42:08: 12000000 INFO @ Sat, 11 Dec 2021 14:42:10: 19000000 INFO @ Sat, 11 Dec 2021 14:42:13: 13000000 INFO @ Sat, 11 Dec 2021 14:42:14: 6000000 INFO @ Sat, 11 Dec 2021 14:42:15: 20000000 INFO @ Sat, 11 Dec 2021 14:42:18: 14000000 INFO @ Sat, 11 Dec 2021 14:42:19: 7000000 INFO @ Sat, 11 Dec 2021 14:42:20: 21000000 INFO @ Sat, 11 Dec 2021 14:42:23: 15000000 INFO @ Sat, 11 Dec 2021 14:42:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:42:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:42:23: #1 total tags in treatment: 9017175 INFO @ Sat, 11 Dec 2021 14:42:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:42:23: #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 14:42:23: #1 tags after filtering in treatment: 7099478 INFO @ Sat, 11 Dec 2021 14:42:23: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:42:23: #1 finished! INFO @ Sat, 11 Dec 2021 14:42:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:42:24: #2 number of paired peaks: 1451 INFO @ Sat, 11 Dec 2021 14:42:24: start model_add_line... INFO @ Sat, 11 Dec 2021 14:42:24: start X-correlation... INFO @ Sat, 11 Dec 2021 14:42:24: end of X-cor INFO @ Sat, 11 Dec 2021 14:42:24: #2 finished! INFO @ Sat, 11 Dec 2021 14:42:24: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 14:42:24: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 14:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.05_model.r WARNING @ Sat, 11 Dec 2021 14:42:24: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:42:24: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 14:42:24: #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 14:42:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:42:25: 8000000 INFO @ Sat, 11 Dec 2021 14:42:28: 16000000 INFO @ Sat, 11 Dec 2021 14:42:31: 9000000 INFO @ Sat, 11 Dec 2021 14:42:33: 17000000 INFO @ Sat, 11 Dec 2021 14:42:37: 10000000 INFO @ Sat, 11 Dec 2021 14:42:38: 18000000 INFO @ Sat, 11 Dec 2021 14:42:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:42:43: 19000000 INFO @ Sat, 11 Dec 2021 14:42:43: 11000000 INFO @ Sat, 11 Dec 2021 14:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.05_summits.bed INFO @ Sat, 11 Dec 2021 14:42:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8904 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:42:48: 20000000 INFO @ Sat, 11 Dec 2021 14:42:49: 12000000 INFO @ Sat, 11 Dec 2021 14:42:53: 21000000 INFO @ Sat, 11 Dec 2021 14:42:55: 13000000 INFO @ Sat, 11 Dec 2021 14:42:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:42:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:42:56: #1 total tags in treatment: 9017175 INFO @ Sat, 11 Dec 2021 14:42:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:42:56: #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 14:42:56: #1 tags after filtering in treatment: 7099478 INFO @ Sat, 11 Dec 2021 14:42:56: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:42:56: #1 finished! INFO @ Sat, 11 Dec 2021 14:42:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:42:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:42:56: #2 number of paired peaks: 1451 INFO @ Sat, 11 Dec 2021 14:42:56: start model_add_line... INFO @ Sat, 11 Dec 2021 14:42:56: start X-correlation... INFO @ Sat, 11 Dec 2021 14:42:56: end of X-cor INFO @ Sat, 11 Dec 2021 14:42:56: #2 finished! INFO @ Sat, 11 Dec 2021 14:42:56: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 14:42:56: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 14:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.10_model.r WARNING @ Sat, 11 Dec 2021 14:42:56: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:42:56: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 14:42:56: #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 14:42:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:43:01: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:43:06: 15000000 INFO @ Sat, 11 Dec 2021 14:43:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:43:12: 16000000 INFO @ Sat, 11 Dec 2021 14:43:17: 17000000 INFO @ Sat, 11 Dec 2021 14:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.10_summits.bed INFO @ Sat, 11 Dec 2021 14:43:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4409 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:43:23: 18000000 INFO @ Sat, 11 Dec 2021 14:43:29: 19000000 INFO @ Sat, 11 Dec 2021 14:43:35: 20000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:43:40: 21000000 INFO @ Sat, 11 Dec 2021 14:43:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:43:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:43:43: #1 total tags in treatment: 9017175 INFO @ Sat, 11 Dec 2021 14:43:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:43:43: #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 14:43:43: #1 tags after filtering in treatment: 7099478 INFO @ Sat, 11 Dec 2021 14:43:43: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:43:43: #1 finished! INFO @ Sat, 11 Dec 2021 14:43:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:43:44: #2 number of paired peaks: 1451 INFO @ Sat, 11 Dec 2021 14:43:44: start model_add_line... INFO @ Sat, 11 Dec 2021 14:43:44: start X-correlation... INFO @ Sat, 11 Dec 2021 14:43:44: end of X-cor INFO @ Sat, 11 Dec 2021 14:43:44: #2 finished! INFO @ Sat, 11 Dec 2021 14:43:44: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 14:43:44: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 14:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.20_model.r WARNING @ Sat, 11 Dec 2021 14:43:44: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:43:44: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 14:43:44: #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 14:43:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:43:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:43:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103813/SRX9103813.20_summits.bed INFO @ Sat, 11 Dec 2021 14:44:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1066 records, 4 fields): 6 millis CompletedMACS2peakCalling