Job ID = 5720378 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,075,858 reads read : 14,075,858 reads written : 14,075,858 2020-04-15T15:18:05 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 13,930,464 reads read : 13,930,464 reads written : 13,930,464 spots read : 14,125,279 reads read : 14,125,279 reads written : 14,125,279 spots read : 13,865,010 reads read : 13,865,010 reads written : 13,865,010 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:06 55996611 reads; of these: 55996611 (100.00%) were unpaired; of these: 1470697 (2.63%) aligned 0 times 38478891 (68.72%) aligned exactly 1 time 16047023 (28.66%) aligned >1 times 97.37% overall alignment rate Time searching: 00:18:06 Overall time: 00:18:06 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_rmdupse_core] 24114838 / 54525914 = 0.4423 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 00:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.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 @ Thu, 16 Apr 2020 00:57:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:57:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:57:37: 1000000 INFO @ Thu, 16 Apr 2020 00:57:42: 2000000 INFO @ Thu, 16 Apr 2020 00:57:47: 3000000 INFO @ Thu, 16 Apr 2020 00:57:52: 4000000 INFO @ Thu, 16 Apr 2020 00:57:58: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 00:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.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 @ Thu, 16 Apr 2020 00:58:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:58:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:58:03: 6000000 INFO @ Thu, 16 Apr 2020 00:58:06: 1000000 INFO @ Thu, 16 Apr 2020 00:58:09: 7000000 INFO @ Thu, 16 Apr 2020 00:58:11: 2000000 INFO @ Thu, 16 Apr 2020 00:58:14: 8000000 INFO @ Thu, 16 Apr 2020 00:58:16: 3000000 INFO @ Thu, 16 Apr 2020 00:58:20: 9000000 INFO @ Thu, 16 Apr 2020 00:58:21: 4000000 INFO @ Thu, 16 Apr 2020 00:58:25: 10000000 INFO @ Thu, 16 Apr 2020 00:58:25: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 00:58:30: 6000000 INFO @ Thu, 16 Apr 2020 00:58:30: 11000000 INFO @ Thu, 16 Apr 2020 00:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.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 @ Thu, 16 Apr 2020 00:58:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:58:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:58:35: 7000000 INFO @ Thu, 16 Apr 2020 00:58:36: 12000000 INFO @ Thu, 16 Apr 2020 00:58:37: 1000000 INFO @ Thu, 16 Apr 2020 00:58:40: 8000000 INFO @ Thu, 16 Apr 2020 00:58:41: 13000000 INFO @ Thu, 16 Apr 2020 00:58:42: 2000000 INFO @ Thu, 16 Apr 2020 00:58:45: 9000000 INFO @ Thu, 16 Apr 2020 00:58:46: 3000000 INFO @ Thu, 16 Apr 2020 00:58:47: 14000000 INFO @ Thu, 16 Apr 2020 00:58:50: 10000000 INFO @ Thu, 16 Apr 2020 00:58:51: 4000000 INFO @ Thu, 16 Apr 2020 00:58:52: 15000000 INFO @ Thu, 16 Apr 2020 00:58:55: 11000000 INFO @ Thu, 16 Apr 2020 00:58:56: 5000000 INFO @ Thu, 16 Apr 2020 00:58:58: 16000000 INFO @ Thu, 16 Apr 2020 00:59:01: 12000000 INFO @ Thu, 16 Apr 2020 00:59:01: 6000000 INFO @ Thu, 16 Apr 2020 00:59:03: 17000000 INFO @ Thu, 16 Apr 2020 00:59:06: 13000000 INFO @ Thu, 16 Apr 2020 00:59:06: 7000000 INFO @ Thu, 16 Apr 2020 00:59:08: 18000000 INFO @ Thu, 16 Apr 2020 00:59:11: 14000000 INFO @ Thu, 16 Apr 2020 00:59:11: 8000000 INFO @ Thu, 16 Apr 2020 00:59:14: 19000000 INFO @ Thu, 16 Apr 2020 00:59:16: 15000000 INFO @ Thu, 16 Apr 2020 00:59:16: 9000000 INFO @ Thu, 16 Apr 2020 00:59:19: 20000000 INFO @ Thu, 16 Apr 2020 00:59:21: 16000000 INFO @ Thu, 16 Apr 2020 00:59:21: 10000000 INFO @ Thu, 16 Apr 2020 00:59:25: 21000000 INFO @ Thu, 16 Apr 2020 00:59:26: 17000000 INFO @ Thu, 16 Apr 2020 00:59:26: 11000000 INFO @ Thu, 16 Apr 2020 00:59:30: 22000000 INFO @ Thu, 16 Apr 2020 00:59:30: 18000000 INFO @ Thu, 16 Apr 2020 00:59:31: 12000000 INFO @ Thu, 16 Apr 2020 00:59:36: 19000000 INFO @ Thu, 16 Apr 2020 00:59:36: 23000000 INFO @ Thu, 16 Apr 2020 00:59:36: 13000000 INFO @ Thu, 16 Apr 2020 00:59:41: 20000000 INFO @ Thu, 16 Apr 2020 00:59:41: 24000000 INFO @ Thu, 16 Apr 2020 00:59:41: 14000000 INFO @ Thu, 16 Apr 2020 00:59:45: 21000000 INFO @ Thu, 16 Apr 2020 00:59:46: 15000000 INFO @ Thu, 16 Apr 2020 00:59:47: 25000000 INFO @ Thu, 16 Apr 2020 00:59:50: 22000000 INFO @ Thu, 16 Apr 2020 00:59:51: 16000000 INFO @ Thu, 16 Apr 2020 00:59:52: 26000000 INFO @ Thu, 16 Apr 2020 00:59:55: 23000000 INFO @ Thu, 16 Apr 2020 00:59:56: 17000000 INFO @ Thu, 16 Apr 2020 00:59:58: 27000000 INFO @ Thu, 16 Apr 2020 01:00:00: 24000000 INFO @ Thu, 16 Apr 2020 01:00:01: 18000000 INFO @ Thu, 16 Apr 2020 01:00:03: 28000000 INFO @ Thu, 16 Apr 2020 01:00:05: 25000000 INFO @ Thu, 16 Apr 2020 01:00:06: 19000000 INFO @ Thu, 16 Apr 2020 01:00:09: 29000000 INFO @ Thu, 16 Apr 2020 01:00:10: 26000000 INFO @ Thu, 16 Apr 2020 01:00:10: 20000000 INFO @ Thu, 16 Apr 2020 01:00:14: 30000000 INFO @ Thu, 16 Apr 2020 01:00:15: 27000000 INFO @ Thu, 16 Apr 2020 01:00:15: 21000000 INFO @ Thu, 16 Apr 2020 01:00:16: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:00:16: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:00:16: #1 total tags in treatment: 30411076 INFO @ Thu, 16 Apr 2020 01:00:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:00:17: #1 tags after filtering in treatment: 30411076 INFO @ Thu, 16 Apr 2020 01:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:17: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:19: #2 number of paired peaks: 597 WARNING @ Thu, 16 Apr 2020 01:00:19: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Thu, 16 Apr 2020 01:00:19: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:19: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:19: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:19: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:19: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 01:00:19: #2 alternative fragment length(s) may be 1,47,62 bps INFO @ Thu, 16 Apr 2020 01:00:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.05_model.r WARNING @ Thu, 16 Apr 2020 01:00:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:00:19: #2 You may need to consider one of the other alternative d(s): 1,47,62 WARNING @ Thu, 16 Apr 2020 01:00:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:00:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:20: 28000000 INFO @ Thu, 16 Apr 2020 01:00:20: 22000000 INFO @ Thu, 16 Apr 2020 01:00:25: 29000000 INFO @ Thu, 16 Apr 2020 01:00:25: 23000000 INFO @ Thu, 16 Apr 2020 01:00:30: 30000000 INFO @ Thu, 16 Apr 2020 01:00:30: 24000000 INFO @ Thu, 16 Apr 2020 01:00:32: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:00:32: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:00:32: #1 total tags in treatment: 30411076 INFO @ Thu, 16 Apr 2020 01:00:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:00:32: #1 tags after filtering in treatment: 30411076 INFO @ Thu, 16 Apr 2020 01:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:32: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:34: #2 number of paired peaks: 597 WARNING @ Thu, 16 Apr 2020 01:00:34: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Thu, 16 Apr 2020 01:00:34: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:35: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:35: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:35: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:35: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 01:00:35: #2 alternative fragment length(s) may be 1,47,62 bps INFO @ Thu, 16 Apr 2020 01:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.10_model.r WARNING @ Thu, 16 Apr 2020 01:00:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:00:35: #2 You may need to consider one of the other alternative d(s): 1,47,62 WARNING @ Thu, 16 Apr 2020 01:00:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:00:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:35: 25000000 INFO @ Thu, 16 Apr 2020 01:00:39: 26000000 INFO @ Thu, 16 Apr 2020 01:00:44: 27000000 INFO @ Thu, 16 Apr 2020 01:00:49: 28000000 INFO @ Thu, 16 Apr 2020 01:00:53: 29000000 INFO @ Thu, 16 Apr 2020 01:00:58: 30000000 INFO @ Thu, 16 Apr 2020 01:01:00: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:01:00: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:01:00: #1 total tags in treatment: 30411076 INFO @ Thu, 16 Apr 2020 01:01:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:01:00: #1 tags after filtering in treatment: 30411076 INFO @ Thu, 16 Apr 2020 01:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:00: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:02: #2 number of paired peaks: 597 WARNING @ Thu, 16 Apr 2020 01:01:02: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Thu, 16 Apr 2020 01:01:02: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:02: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:02: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:02: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:02: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 01:01:02: #2 alternative fragment length(s) may be 1,47,62 bps INFO @ Thu, 16 Apr 2020 01:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.20_model.r WARNING @ Thu, 16 Apr 2020 01:01:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:01:02: #2 You may need to consider one of the other alternative d(s): 1,47,62 WARNING @ Thu, 16 Apr 2020 01:01:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:01:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.05_summits.bed INFO @ Thu, 16 Apr 2020 01:01:27: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.10_summits.bed INFO @ Thu, 16 Apr 2020 01:01:45: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:01:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3548058/ERX3548058.20_summits.bed INFO @ Thu, 16 Apr 2020 01:02:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。