[2024-01-24 11:59:05,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:05,103] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:05,103] [INFO] DQC Reference Directory: /var/lib/cwl/stgb53d7fab-a4ff-4398-bce9-3d804729203e/dqc_reference
[2024-01-24 11:59:06,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:06,280] [INFO] Task started: Prodigal
[2024-01-24 11:59:06,280] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2736e52-844d-477f-b0e7-6c0ec4def704/GCF_008014345.1_ASM801434v1_genomic.fna.gz | prodigal -d GCF_008014345.1_ASM801434v1_genomic.fna/cds.fna -a GCF_008014345.1_ASM801434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:16,438] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:16,439] [INFO] Task started: HMMsearch
[2024-01-24 11:59:16,439] [INFO] Running command: hmmsearch --tblout GCF_008014345.1_ASM801434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb53d7fab-a4ff-4398-bce9-3d804729203e/dqc_reference/reference_markers.hmm GCF_008014345.1_ASM801434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:16,717] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:16,719] [INFO] Found 6/6 markers.
[2024-01-24 11:59:17,024] [INFO] Query marker FASTA was written to GCF_008014345.1_ASM801434v1_genomic.fna/markers.fasta
[2024-01-24 11:59:17,025] [INFO] Task started: Blastn
[2024-01-24 11:59:17,025] [INFO] Running command: blastn -query GCF_008014345.1_ASM801434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb53d7fab-a4ff-4398-bce9-3d804729203e/dqc_reference/reference_markers.fasta -out GCF_008014345.1_ASM801434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:17,803] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:17,812] [INFO] Selected 28 target genomes.
[2024-01-24 11:59:17,813] [INFO] Target genome list was writen to GCF_008014345.1_ASM801434v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:17,865] [INFO] Task started: fastANI
[2024-01-24 11:59:17,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2736e52-844d-477f-b0e7-6c0ec4def704/GCF_008014345.1_ASM801434v1_genomic.fna.gz --refList GCF_008014345.1_ASM801434v1_genomic.fna/target_genomes.txt --output GCF_008014345.1_ASM801434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:37,101] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:37,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb53d7fab-a4ff-4398-bce9-3d804729203e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:37,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb53d7fab-a4ff-4398-bce9-3d804729203e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:37,121] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:37,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:37,122] [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
Pelomicrobium methylotrophicum	strain=SM250	GCA_008014345.1	2602750	2602750	type	True	100.0	1074	1077	95	conclusive
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.0931	158	1077	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.0757	157	1077	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	76.6899	204	1077	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	76.5944	112	1077	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.5743	111	1077	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.5145	144	1077	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.5123	121	1077	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.5005	158	1077	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	76.384	143	1077	95	below_threshold
Tepidimonas charontis	strain=SPSP-6	GCA_007556685.1	2267262	2267262	type	True	76.3546	81	1077	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	76.3292	80	1077	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	76.0745	121	1077	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.0301	100	1077	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	75.9432	134	1077	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	75.8628	85	1077	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	75.7455	54	1077	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	75.7388	73	1077	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	75.6391	58	1077	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	75.5587	51	1077	95	below_threshold
Paraburkholderia ribeironis	strain=STM 7296	GCA_900019265.2	1247936	1247936	type	True	75.4805	73	1077	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	75.4507	63	1077	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:37,123] [INFO] DFAST Taxonomy check result was written to GCF_008014345.1_ASM801434v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:37,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:37,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:37,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb53d7fab-a4ff-4398-bce9-3d804729203e/dqc_reference/checkm_data
[2024-01-24 11:59:37,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:37,163] [INFO] Task started: CheckM
[2024-01-24 11:59:37,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008014345.1_ASM801434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008014345.1_ASM801434v1_genomic.fna/checkm_input GCF_008014345.1_ASM801434v1_genomic.fna/checkm_result
[2024-01-24 12:00:09,131] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:09,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:09,157] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:09,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:09,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008014345.1_ASM801434v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:09,158] [INFO] Task started: Blastn
[2024-01-24 12:00:09,159] [INFO] Running command: blastn -query GCF_008014345.1_ASM801434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb53d7fab-a4ff-4398-bce9-3d804729203e/dqc_reference/reference_markers_gtdb.fasta -out GCF_008014345.1_ASM801434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:10,589] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:10,593] [INFO] Selected 27 target genomes.
[2024-01-24 12:00:10,594] [INFO] Target genome list was writen to GCF_008014345.1_ASM801434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:10,651] [INFO] Task started: fastANI
[2024-01-24 12:00:10,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2736e52-844d-477f-b0e7-6c0ec4def704/GCF_008014345.1_ASM801434v1_genomic.fna.gz --refList GCF_008014345.1_ASM801434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008014345.1_ASM801434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:28,084] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:28,110] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:28,110] [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
GCF_008014345.1	s__Pelomicrobium methylotrophicum	100.0	1074	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA6910;g__Pelomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016183615.1	s__JACPEG01 sp016183615	77.7116	289	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA6910;g__JACPEG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967275.1	s__Sulfuritortus calidifontis	77.0848	158	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016791205.1	s__Desulfobacillus sp016791205	76.9117	136	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770655.1	s__2-12-FULL-68-20 sp001770655	76.8808	149	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-68-20	95.0	99.77	99.77	0.95	0.95	2	-
GCA_016199485.1	s__JACQGO01 sp016199485	76.8685	131	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__JACQGO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720425.1	s__CAIWHR01 sp016720425	76.8415	139	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCA_001724855.1	s__SCN-69-89 sp001724855	76.712	127	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801305.1	s__Thauera_A rhizosphaerae	76.6899	204	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192825.1	s__SG8-41 sp016192825	76.6245	167	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119085.1	s__Nitrosospira sp900119085	76.6165	109	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772925.1	s__PFJX01 sp009772925	76.6128	133	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.99	99.98	1.00	0.99	4	-
GCA_001771935.1	s__SG8-41 sp001771935	76.5888	168	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873935.1	s__PFJX01 sp016873935	76.5284	126	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898645.1	s__SCN-69-89 sp001898645	76.5012	163	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.96	99.96	0.96	0.96	2	-
GCF_003337735.1	s__Thioalbus denitrificans	76.4742	160	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826155.1	s__CADEDU01 sp902826155	76.4554	117	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CADEDU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019137045.1	s__JAGVSZ01 sp019137045	76.4447	160	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__JAGVSZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860355.1	s__2-12-FULL-64-23 sp014860355	76.4085	118	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464765.1	s__Ga0077526 sp001464765	76.2364	139	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124745.1	s__Thiobacillus sp016124745	76.1335	85	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330945.1	s__UBA2250 sp011330945	76.1238	123	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	99.90	99.90	0.95	0.95	2	-
GCA_016125475.1	s__Ga0077526 sp016125475	75.9634	115	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Ga0077523;g__Ga0077526	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801985.1	s__Steroidobacter_A sp016801985	75.4507	63	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013911085.1	s__Aquitalea magnusonii_C	75.2249	53	1077	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:28,112] [INFO] GTDB search result was written to GCF_008014345.1_ASM801434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:28,113] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:28,120] [INFO] DFAST_QC result json was written to GCF_008014345.1_ASM801434v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:28,120] [INFO] DFAST_QC completed!
[2024-01-24 12:00:28,120] [INFO] Total running time: 0h1m23s