[2024-01-24 13:17:13,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg7779a35f-3e7d-4a70-af72-836a45406f6b/dqc_reference
[2024-01-24 13:17:15,170] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,171] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,171] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f996658-4d53-4186-a926-6c7253a6761a/GCF_000256565.1_Asm2.0_genomic.fna.gz | prodigal -d GCF_000256565.1_Asm2.0_genomic.fna/cds.fna -a GCF_000256565.1_Asm2.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:28,685] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:28,685] [INFO] Task started: HMMsearch
[2024-01-24 13:17:28,685] [INFO] Running command: hmmsearch --tblout GCF_000256565.1_Asm2.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7779a35f-3e7d-4a70-af72-836a45406f6b/dqc_reference/reference_markers.hmm GCF_000256565.1_Asm2.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:28,995] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:28,997] [INFO] Found 6/6 markers.
[2024-01-24 13:17:29,049] [INFO] Query marker FASTA was written to GCF_000256565.1_Asm2.0_genomic.fna/markers.fasta
[2024-01-24 13:17:29,049] [INFO] Task started: Blastn
[2024-01-24 13:17:29,050] [INFO] Running command: blastn -query GCF_000256565.1_Asm2.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg7779a35f-3e7d-4a70-af72-836a45406f6b/dqc_reference/reference_markers.fasta -out GCF_000256565.1_Asm2.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:30,027] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:30,031] [INFO] Selected 17 target genomes.
[2024-01-24 13:17:30,031] [INFO] Target genome list was writen to GCF_000256565.1_Asm2.0_genomic.fna/target_genomes.txt
[2024-01-24 13:17:30,068] [INFO] Task started: fastANI
[2024-01-24 13:17:30,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f996658-4d53-4186-a926-6c7253a6761a/GCF_000256565.1_Asm2.0_genomic.fna.gz --refList GCF_000256565.1_Asm2.0_genomic.fna/target_genomes.txt --output GCF_000256565.1_Asm2.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:48,488] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:48,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7779a35f-3e7d-4a70-af72-836a45406f6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:48,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7779a35f-3e7d-4a70-af72-836a45406f6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:48,503] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:48,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:48,503] [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
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	100.0	1262	1284	95	conclusive
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	91.2786	1052	1284	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	87.2227	983	1284	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	83.5055	801	1284	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	83.1444	803	1284	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	82.9895	865	1284	95	below_threshold
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	82.5279	783	1284	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	82.4787	790	1284	95	below_threshold
Herbaspirillum chlorophenolicum	strain=CPW301	GCA_001189955.1	211589	211589	type	True	82.4626	801	1284	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	81.0952	707	1284	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	80.7512	561	1284	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	80.3916	580	1284	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	79.7807	501	1284	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.6598	435	1284	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	79.436	459	1284	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	79.3602	419	1284	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	78.7236	364	1284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:48,505] [INFO] DFAST Taxonomy check result was written to GCF_000256565.1_Asm2.0_genomic.fna/tc_result.tsv
[2024-01-24 13:17:48,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:48,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:48,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7779a35f-3e7d-4a70-af72-836a45406f6b/dqc_reference/checkm_data
[2024-01-24 13:17:48,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:48,561] [INFO] Task started: CheckM
[2024-01-24 13:17:48,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000256565.1_Asm2.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000256565.1_Asm2.0_genomic.fna/checkm_input GCF_000256565.1_Asm2.0_genomic.fna/checkm_result
[2024-01-24 13:18:30,938] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:30,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:30,962] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:30,962] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:30,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000256565.1_Asm2.0_genomic.fna/markers.fasta)
[2024-01-24 13:18:30,963] [INFO] Task started: Blastn
[2024-01-24 13:18:30,963] [INFO] Running command: blastn -query GCF_000256565.1_Asm2.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg7779a35f-3e7d-4a70-af72-836a45406f6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000256565.1_Asm2.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:32,572] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:32,577] [INFO] Selected 6 target genomes.
[2024-01-24 13:18:32,577] [INFO] Target genome list was writen to GCF_000256565.1_Asm2.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:32,587] [INFO] Task started: fastANI
[2024-01-24 13:18:32,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f996658-4d53-4186-a926-6c7253a6761a/GCF_000256565.1_Asm2.0_genomic.fna.gz --refList GCF_000256565.1_Asm2.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000256565.1_Asm2.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:40,761] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:40,775] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:40,776] [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_000256565.1	s__Herbaspirillum lusitanum	100.0	1262	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004563925.1	s__Herbaspirillum sp004563925	92.279	1068	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	99.99	0.98	0.95	4	-
GCF_001267925.1	s__Herbaspirillum hiltneri	91.2678	1053	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.60	97.60	0.89	0.89	2	-
GCF_000282135.1	s__Herbaspirillum sp000282135	87.2788	960	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	87.2358	982	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577615.1	s__Herbaspirillum sp000577615	86.5934	941	1284	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:40,778] [INFO] GTDB search result was written to GCF_000256565.1_Asm2.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:40,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:40,783] [INFO] DFAST_QC result json was written to GCF_000256565.1_Asm2.0_genomic.fna/dqc_result.json
[2024-01-24 13:18:40,784] [INFO] DFAST_QC completed!
[2024-01-24 13:18:40,784] [INFO] Total running time: 0h1m27s