[2023-06-29 22:59:11,738] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:59:11,740] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:59:11,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6f03ff2-0aea-42c6-83ad-24da2e49a317/dqc_reference
[2023-06-29 22:59:12,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:59:12,949] [INFO] Task started: Prodigal
[2023-06-29 22:59:12,949] [INFO] Running command: gunzip -c /var/lib/cwl/stgeee53751-d5a7-423a-b37b-b938280d8403/GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna.gz | prodigal -d GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/cds.fna -a GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:59:20,940] [INFO] Task succeeded: Prodigal
[2023-06-29 22:59:20,940] [INFO] Task started: HMMsearch
[2023-06-29 22:59:20,940] [INFO] Running command: hmmsearch --tblout GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6f03ff2-0aea-42c6-83ad-24da2e49a317/dqc_reference/reference_markers.hmm GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:59:21,271] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:59:21,272] [INFO] Found 6/6 markers.
[2023-06-29 22:59:21,305] [INFO] Query marker FASTA was written to GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/markers.fasta
[2023-06-29 22:59:21,305] [INFO] Task started: Blastn
[2023-06-29 22:59:21,305] [INFO] Running command: blastn -query GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6f03ff2-0aea-42c6-83ad-24da2e49a317/dqc_reference/reference_markers.fasta -out GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:59:22,024] [INFO] Task succeeded: Blastn
[2023-06-29 22:59:22,028] [INFO] Selected 15 target genomes.
[2023-06-29 22:59:22,028] [INFO] Target genome list was writen to GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/target_genomes.txt
[2023-06-29 22:59:22,032] [INFO] Task started: fastANI
[2023-06-29 22:59:22,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgeee53751-d5a7-423a-b37b-b938280d8403/GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna.gz --refList GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/target_genomes.txt --output GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:59:30,006] [INFO] Task succeeded: fastANI
[2023-06-29 22:59:30,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6f03ff2-0aea-42c6-83ad-24da2e49a317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:59:30,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6f03ff2-0aea-42c6-83ad-24da2e49a317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:59:30,015] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:59:30,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:59:30,015] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	82.9941	590	934	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	78.7531	317	934	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	78.2285	176	934	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.0771	167	934	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	76.9018	105	934	95	below_threshold
Chlorobaculum tepidum	strain=TLS	GCA_000006985.1	1097	1097	type	True	76.5797	77	934	95	below_threshold
Chlorobaculum limnaeum	strain=DSM 1677	GCA_001747405.1	274537	274537	type	True	76.361	86	934	95	below_threshold
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	76.334	88	934	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:59:30,018] [INFO] DFAST Taxonomy check result was written to GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/tc_result.tsv
[2023-06-29 22:59:30,018] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:59:30,019] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:59:30,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6f03ff2-0aea-42c6-83ad-24da2e49a317/dqc_reference/checkm_data
[2023-06-29 22:59:30,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:59:30,054] [INFO] Task started: CheckM
[2023-06-29 22:59:30,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/checkm_input GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/checkm_result
[2023-06-29 23:00:00,207] [INFO] Task succeeded: CheckM
[2023-06-29 23:00:00,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 23:00:00,232] [INFO] ===== Completeness check finished =====
[2023-06-29 23:00:00,233] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:00:00,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/markers.fasta)
[2023-06-29 23:00:00,233] [INFO] Task started: Blastn
[2023-06-29 23:00:00,234] [INFO] Running command: blastn -query GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6f03ff2-0aea-42c6-83ad-24da2e49a317/dqc_reference/reference_markers_gtdb.fasta -out GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:00:01,174] [INFO] Task succeeded: Blastn
[2023-06-29 23:00:01,178] [INFO] Selected 15 target genomes.
[2023-06-29 23:00:01,178] [INFO] Target genome list was writen to GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:00:01,221] [INFO] Task started: fastANI
[2023-06-29 23:00:01,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgeee53751-d5a7-423a-b37b-b938280d8403/GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna.gz --refList GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/target_genomes_gtdb.txt --output GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:00:10,287] [INFO] Task succeeded: fastANI
[2023-06-29 23:00:10,304] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:00:10,304] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_903882665.1	s__Chlorobium sp903882665	99.9689	879	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.83	0.90	0.84	7	conclusive
GCA_903840935.1	s__Chlorobium sp903840935	93.0378	539	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.22	98.87	0.67	0.63	5	-
GCA_903851535.1	s__Chlorobium sp903851535	89.1254	445	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.27	98.97	0.76	0.73	4	-
GCA_903939765.1	s__Chlorobium sp903939765	87.534	642	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.90	99.86	0.94	0.94	3	-
GCA_903824295.1	s__Chlorobium sp903824295	87.3073	621	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.79	99.65	0.92	0.89	3	-
GCA_903871235.1	s__Chlorobium sp903871235	86.4906	620	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.74	99.66	0.91	0.89	5	-
GCA_903917955.1	s__Chlorobium sp903917955	86.239	460	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.38	99.38	0.85	0.85	2	-
GCA_903822595.1	s__Chlorobium sp903822595	85.8082	628	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.84	99.77	0.94	0.93	3	-
GCA_903838025.1	s__Chlorobium sp903838025	85.2989	456	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903836465.1	s__Chlorobium sp903836465	80.4817	441	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.30	97.63	0.95	0.90	12	-
GCA_903887845.1	s__Chlorobium sp903887845	80.4765	438	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.96	99.96	0.95	0.95	2	-
GCA_903994455.1	s__Chlorobium sp903994455	80.4463	420	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.65	99.40	0.86	0.85	13	-
GCA_903937835.1	s__Chlorobium sp903937835	80.3746	437	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.77	99.60	0.93	0.86	6	-
GCA_005862225.1	s__Chlorobium sp005862225	80.0625	386	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903994525.1	s__Chlorobium sp903994525	79.5094	319	934	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.83	98.94	0.92	0.84	27	-
--------------------------------------------------------------------------------
[2023-06-29 23:00:10,307] [INFO] GTDB search result was written to GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/result_gtdb.tsv
[2023-06-29 23:00:10,307] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:00:10,311] [INFO] DFAST_QC result json was written to GCA_903835515.1_freshwater_MAG_---_Ki2-D4_bin-0122_genomic.fna/dqc_result.json
[2023-06-29 23:00:10,311] [INFO] DFAST_QC completed!
[2023-06-29 23:00:10,312] [INFO] Total running time: 0h0m59s