[2024-01-25 18:43:50,753] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:50,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:50,754] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf738b1a-d40b-4ad8-a351-294aff8ed868/dqc_reference
[2024-01-25 18:43:51,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:51,951] [INFO] Task started: Prodigal
[2024-01-25 18:43:51,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg71db49d4-5a9a-410e-b90c-f965d932476e/GCF_002213415.1_ASM221341v1_genomic.fna.gz | prodigal -d GCF_002213415.1_ASM221341v1_genomic.fna/cds.fna -a GCF_002213415.1_ASM221341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:07,562] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:07,562] [INFO] Task started: HMMsearch
[2024-01-25 18:44:07,563] [INFO] Running command: hmmsearch --tblout GCF_002213415.1_ASM221341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf738b1a-d40b-4ad8-a351-294aff8ed868/dqc_reference/reference_markers.hmm GCF_002213415.1_ASM221341v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:07,849] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:07,850] [INFO] Found 6/6 markers.
[2024-01-25 18:44:07,893] [INFO] Query marker FASTA was written to GCF_002213415.1_ASM221341v1_genomic.fna/markers.fasta
[2024-01-25 18:44:07,893] [INFO] Task started: Blastn
[2024-01-25 18:44:07,894] [INFO] Running command: blastn -query GCF_002213415.1_ASM221341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf738b1a-d40b-4ad8-a351-294aff8ed868/dqc_reference/reference_markers.fasta -out GCF_002213415.1_ASM221341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:08,925] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:08,929] [INFO] Selected 15 target genomes.
[2024-01-25 18:44:08,930] [INFO] Target genome list was writen to GCF_002213415.1_ASM221341v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:08,934] [INFO] Task started: fastANI
[2024-01-25 18:44:08,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg71db49d4-5a9a-410e-b90c-f965d932476e/GCF_002213415.1_ASM221341v1_genomic.fna.gz --refList GCF_002213415.1_ASM221341v1_genomic.fna/target_genomes.txt --output GCF_002213415.1_ASM221341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:27,802] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:27,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf738b1a-d40b-4ad8-a351-294aff8ed868/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:27,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf738b1a-d40b-4ad8-a351-294aff8ed868/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:27,813] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:27,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:27,813] [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
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	100.0	1828	1830	95	conclusive
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	87.4512	1211	1830	95	below_threshold
Herbaspirillum chlorophenolicum	strain=CPW301	GCA_001189955.1	211589	211589	type	True	87.4291	1204	1830	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	85.9241	1237	1830	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	85.9099	1226	1830	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	85.7036	1233	1830	95	below_threshold
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	85.6802	1241	1830	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	85.5791	1242	1830	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	85.5597	1249	1830	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	85.1055	1144	1830	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	85.0693	1172	1830	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	82.9658	855	1830	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	80.4678	582	1830	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	80.0222	667	1830	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	79.9645	645	1830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:27,814] [INFO] DFAST Taxonomy check result was written to GCF_002213415.1_ASM221341v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:27,815] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:27,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:27,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf738b1a-d40b-4ad8-a351-294aff8ed868/dqc_reference/checkm_data
[2024-01-25 18:44:27,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:27,869] [INFO] Task started: CheckM
[2024-01-25 18:44:27,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002213415.1_ASM221341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002213415.1_ASM221341v1_genomic.fna/checkm_input GCF_002213415.1_ASM221341v1_genomic.fna/checkm_result
[2024-01-25 18:45:17,237] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:17,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:17,257] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:17,257] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:17,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002213415.1_ASM221341v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:17,258] [INFO] Task started: Blastn
[2024-01-25 18:45:17,258] [INFO] Running command: blastn -query GCF_002213415.1_ASM221341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf738b1a-d40b-4ad8-a351-294aff8ed868/dqc_reference/reference_markers_gtdb.fasta -out GCF_002213415.1_ASM221341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:19,404] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:19,407] [INFO] Selected 11 target genomes.
[2024-01-25 18:45:19,407] [INFO] Target genome list was writen to GCF_002213415.1_ASM221341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:19,423] [INFO] Task started: fastANI
[2024-01-25 18:45:19,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg71db49d4-5a9a-410e-b90c-f965d932476e/GCF_002213415.1_ASM221341v1_genomic.fna.gz --refList GCF_002213415.1_ASM221341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002213415.1_ASM221341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:35,739] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:35,747] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:35,747] [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_002213415.1	s__Herbaspirillum robiniae	100.0	1828	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	conclusive
GCF_017814915.1	s__Herbaspirillum sp017814915	89.8088	1411	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	88.9632	1170	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	88.5453	1159	1830	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	88.228	1185	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	99.71	99.15	0.99	0.96	4	-
GCF_016429215.1	s__Herbaspirillum sp016429215	86.2127	1272	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040945.1	s__Herbaspirillum seropedicae	85.9307	1236	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCF_000300975.2	s__Herbaspirillum frisingense	85.6805	1241	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.59	97.42	0.92	0.89	5	-
GCF_002213425.1	s__Herbaspirillum aquaticum	85.598	1240	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.01	95.53	0.89	0.85	3	-
GCF_004367745.1	s__Herbaspirillum huttiense	85.4027	1273	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.45	97.06	0.87	0.86	14	-
GCF_003719195.1	s__Herbaspirillum rubrisubalbicans	85.0759	1171	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.49	96.58	0.87	0.83	8	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:35,751] [INFO] GTDB search result was written to GCF_002213415.1_ASM221341v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:35,751] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:35,760] [INFO] DFAST_QC result json was written to GCF_002213415.1_ASM221341v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:35,761] [INFO] DFAST_QC completed!
[2024-01-25 18:45:35,761] [INFO] Total running time: 0h1m45s