[2024-01-25 20:02:35,732] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:35,734] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:35,734] [INFO] DQC Reference Directory: /var/lib/cwl/stgd938319b-4280-46d7-adaa-77763ad21afd/dqc_reference
[2024-01-25 20:02:36,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:36,892] [INFO] Task started: Prodigal
[2024-01-25 20:02:36,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f64324b-a0b6-4530-bf22-51c35b4c8934/GCF_016632335.1_ASM1663233v1_genomic.fna.gz | prodigal -d GCF_016632335.1_ASM1663233v1_genomic.fna/cds.fna -a GCF_016632335.1_ASM1663233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:59,801] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:59,801] [INFO] Task started: HMMsearch
[2024-01-25 20:02:59,801] [INFO] Running command: hmmsearch --tblout GCF_016632335.1_ASM1663233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd938319b-4280-46d7-adaa-77763ad21afd/dqc_reference/reference_markers.hmm GCF_016632335.1_ASM1663233v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:00,117] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:00,118] [INFO] Found 6/6 markers.
[2024-01-25 20:03:00,172] [INFO] Query marker FASTA was written to GCF_016632335.1_ASM1663233v1_genomic.fna/markers.fasta
[2024-01-25 20:03:00,173] [INFO] Task started: Blastn
[2024-01-25 20:03:00,173] [INFO] Running command: blastn -query GCF_016632335.1_ASM1663233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd938319b-4280-46d7-adaa-77763ad21afd/dqc_reference/reference_markers.fasta -out GCF_016632335.1_ASM1663233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:01,108] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:01,111] [INFO] Selected 24 target genomes.
[2024-01-25 20:03:01,111] [INFO] Target genome list was writen to GCF_016632335.1_ASM1663233v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:01,144] [INFO] Task started: fastANI
[2024-01-25 20:03:01,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f64324b-a0b6-4530-bf22-51c35b4c8934/GCF_016632335.1_ASM1663233v1_genomic.fna.gz --refList GCF_016632335.1_ASM1663233v1_genomic.fna/target_genomes.txt --output GCF_016632335.1_ASM1663233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:26,329] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:26,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd938319b-4280-46d7-adaa-77763ad21afd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:26,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd938319b-4280-46d7-adaa-77763ad21afd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:26,344] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:26,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:26,344] [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
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	100.0	2369	2372	95	conclusive
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	80.0167	678	2372	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.8238	627	2372	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	79.7628	623	2372	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	79.6478	595	2372	95	below_threshold
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	79.575	450	2372	95	below_threshold
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	79.5452	683	2372	95	below_threshold
Herbaspirillum chlorophenolicum	strain=CPW301	GCA_001189955.1	211589	211589	type	True	79.4118	482	2372	95	below_threshold
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	79.3452	483	2372	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	79.3215	405	2372	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	79.2804	504	2372	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	79.2504	516	2372	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	79.2345	514	2372	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.2334	425	2372	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	79.1395	501	2372	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	79.0655	524	2372	95	below_threshold
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	79.059	506	2372	95	below_threshold
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	79.0311	481	2372	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	79.0119	595	2372	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	78.9837	560	2372	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	78.87	469	2372	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	78.8656	485	2372	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	78.8189	467	2372	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	78.4079	557	2372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:26,346] [INFO] DFAST Taxonomy check result was written to GCF_016632335.1_ASM1663233v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:26,346] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:26,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:26,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd938319b-4280-46d7-adaa-77763ad21afd/dqc_reference/checkm_data
[2024-01-25 20:03:26,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:26,418] [INFO] Task started: CheckM
[2024-01-25 20:03:26,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016632335.1_ASM1663233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016632335.1_ASM1663233v1_genomic.fna/checkm_input GCF_016632335.1_ASM1663233v1_genomic.fna/checkm_result
[2024-01-25 20:04:35,526] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:35,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:35,549] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:35,549] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:35,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016632335.1_ASM1663233v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:35,551] [INFO] Task started: Blastn
[2024-01-25 20:04:35,551] [INFO] Running command: blastn -query GCF_016632335.1_ASM1663233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd938319b-4280-46d7-adaa-77763ad21afd/dqc_reference/reference_markers_gtdb.fasta -out GCF_016632335.1_ASM1663233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:37,498] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:37,501] [INFO] Selected 20 target genomes.
[2024-01-25 20:04:37,501] [INFO] Target genome list was writen to GCF_016632335.1_ASM1663233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:37,517] [INFO] Task started: fastANI
[2024-01-25 20:04:37,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f64324b-a0b6-4530-bf22-51c35b4c8934/GCF_016632335.1_ASM1663233v1_genomic.fna.gz --refList GCF_016632335.1_ASM1663233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016632335.1_ASM1663233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:00,781] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:00,793] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:00,794] [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_016632335.1	s__Noviherbaspirillum_A pedocola	100.0	2369	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015352955.1	s__Noviherbaspirillum_A soli	81.5395	905	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019052805.1	s__Noviherbaspirillum_A sp019052805	81.3949	912	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188095.1	s__Noviherbaspirillum humi	80.0505	675	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	79.8068	544	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715495.1	s__Herbaspirillum sp006715495	79.6466	558	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	99.71	99.15	0.99	0.96	4	-
GCF_002213415.1	s__Herbaspirillum robiniae	79.644	596	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	79.5916	509	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635065.1	s__Oxalicibacterium flavum	79.5588	451	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	79.5474	682	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189955.1	s__Herbaspirillum chlorophenolicum	79.413	482	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	99.98	99.98	0.99	0.99	2	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	79.3968	514	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818395.1	s__Noviherbaspirillum autotrophicum	79.2682	509	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040945.1	s__Herbaspirillum seropedicae	79.2568	514	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCF_000382345.1	s__Massilia niastensis	79.0172	594	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282135.1	s__Herbaspirillum sp000282135	79.0027	474	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745265.1	s__Massilia sp000745265	78.8455	587	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	78.8348	488	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614195.1	s__Massilia horti	78.8056	468	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053665.1	s__Pseudoduganella sp003053665	78.7062	594	2372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.77	95.97	0.96	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:00,795] [INFO] GTDB search result was written to GCF_016632335.1_ASM1663233v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:00,796] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:00,799] [INFO] DFAST_QC result json was written to GCF_016632335.1_ASM1663233v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:00,800] [INFO] DFAST_QC completed!
[2024-01-25 20:05:00,800] [INFO] Total running time: 0h2m25s