[2024-01-24 15:03:15,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:15,490] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:15,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e626bed-e603-44a1-bcc4-f1029ee83216/dqc_reference
[2024-01-24 15:03:16,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:16,797] [INFO] Task started: Prodigal
[2024-01-24 15:03:16,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg5669bd38-5320-4f6e-9a68-e5e7018b71de/GCF_003591035.1_ASM359103v1_genomic.fna.gz | prodigal -d GCF_003591035.1_ASM359103v1_genomic.fna/cds.fna -a GCF_003591035.1_ASM359103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:38,838] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:38,838] [INFO] Task started: HMMsearch
[2024-01-24 15:03:38,838] [INFO] Running command: hmmsearch --tblout GCF_003591035.1_ASM359103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e626bed-e603-44a1-bcc4-f1029ee83216/dqc_reference/reference_markers.hmm GCF_003591035.1_ASM359103v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:39,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:39,201] [INFO] Found 6/6 markers.
[2024-01-24 15:03:39,260] [INFO] Query marker FASTA was written to GCF_003591035.1_ASM359103v1_genomic.fna/markers.fasta
[2024-01-24 15:03:39,261] [INFO] Task started: Blastn
[2024-01-24 15:03:39,261] [INFO] Running command: blastn -query GCF_003591035.1_ASM359103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e626bed-e603-44a1-bcc4-f1029ee83216/dqc_reference/reference_markers.fasta -out GCF_003591035.1_ASM359103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:40,139] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:40,142] [INFO] Selected 16 target genomes.
[2024-01-24 15:03:40,142] [INFO] Target genome list was writen to GCF_003591035.1_ASM359103v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:40,169] [INFO] Task started: fastANI
[2024-01-24 15:03:40,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg5669bd38-5320-4f6e-9a68-e5e7018b71de/GCF_003591035.1_ASM359103v1_genomic.fna.gz --refList GCF_003591035.1_ASM359103v1_genomic.fna/target_genomes.txt --output GCF_003591035.1_ASM359103v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:58,488] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:58,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e626bed-e603-44a1-bcc4-f1029ee83216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:58,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e626bed-e603-44a1-bcc4-f1029ee83216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:58,502] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:58,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:58,503] [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 saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	100.0	2162	2164	95	conclusive
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	80.5708	843	2164	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	80.5552	836	2164	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	79.8217	570	2164	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.8211	607	2164	95	below_threshold
Noviherbaspirillum denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	79.7963	656	2164	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	79.1581	586	2164	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	79.1028	469	2164	95	below_threshold
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	78.9639	359	2164	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	78.8517	388	2164	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	78.7593	356	2164	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	78.6953	387	2164	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	78.6925	384	2164	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	78.6659	401	2164	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	78.665	414	2164	95	below_threshold
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	78.5249	421	2164	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:58,505] [INFO] DFAST Taxonomy check result was written to GCF_003591035.1_ASM359103v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:58,505] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:58,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:58,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e626bed-e603-44a1-bcc4-f1029ee83216/dqc_reference/checkm_data
[2024-01-24 15:03:58,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:58,575] [INFO] Task started: CheckM
[2024-01-24 15:03:58,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003591035.1_ASM359103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003591035.1_ASM359103v1_genomic.fna/checkm_input GCF_003591035.1_ASM359103v1_genomic.fna/checkm_result
[2024-01-24 15:05:03,559] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:03,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:03,581] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:03,581] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:03,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003591035.1_ASM359103v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:03,582] [INFO] Task started: Blastn
[2024-01-24 15:05:03,582] [INFO] Running command: blastn -query GCF_003591035.1_ASM359103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e626bed-e603-44a1-bcc4-f1029ee83216/dqc_reference/reference_markers_gtdb.fasta -out GCF_003591035.1_ASM359103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:05,137] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:05,140] [INFO] Selected 13 target genomes.
[2024-01-24 15:05:05,140] [INFO] Target genome list was writen to GCF_003591035.1_ASM359103v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:05,151] [INFO] Task started: fastANI
[2024-01-24 15:05:05,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg5669bd38-5320-4f6e-9a68-e5e7018b71de/GCF_003591035.1_ASM359103v1_genomic.fna.gz --refList GCF_003591035.1_ASM359103v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003591035.1_ASM359103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:20,686] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:20,698] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:20,698] [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_003591035.1	s__Noviherbaspirillum sp003591035	100.0	2163	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001428545.1	s__Noviherbaspirillum sp001428545	81.1366	891	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008929045.1	s__Noviherbaspirillum aerium	80.5699	835	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	80.5656	845	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	79.8241	589	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818395.1	s__Noviherbaspirillum autotrophicum	79.7899	570	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	79.1978	483	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010974945.1	s__Noviherbaspirillum galbum	79.1728	585	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312045.1	s__Noviherbaspirillum massiliense	79.1025	469	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	78.692	412	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267925.1	s__Herbaspirillum hiltneri	78.5122	421	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.60	97.60	0.89	0.89	2	-
GCF_004563925.1	s__Herbaspirillum sp004563925	78.3862	417	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	99.99	0.98	0.95	4	-
GCA_014377845.1	s__CAILRJ01 sp014377845	78.2051	338	2164	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:20,700] [INFO] GTDB search result was written to GCF_003591035.1_ASM359103v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:20,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:20,704] [INFO] DFAST_QC result json was written to GCF_003591035.1_ASM359103v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:20,705] [INFO] DFAST_QC completed!
[2024-01-24 15:05:20,705] [INFO] Total running time: 0h2m5s