[2024-01-25 19:35:05,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:05,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:05,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb809d9c-9c24-4666-92a6-4699ae4e5392/dqc_reference
[2024-01-25 19:35:06,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:06,690] [INFO] Task started: Prodigal
[2024-01-25 19:35:06,691] [INFO] Running command: gunzip -c /var/lib/cwl/stgffc30622-a926-41a3-ad75-b00fc58da97a/GCF_009469765.1_ASM946976v1_genomic.fna.gz | prodigal -d GCF_009469765.1_ASM946976v1_genomic.fna/cds.fna -a GCF_009469765.1_ASM946976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:17,651] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:17,651] [INFO] Task started: HMMsearch
[2024-01-25 19:35:17,651] [INFO] Running command: hmmsearch --tblout GCF_009469765.1_ASM946976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb809d9c-9c24-4666-92a6-4699ae4e5392/dqc_reference/reference_markers.hmm GCF_009469765.1_ASM946976v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:17,882] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:17,883] [INFO] Found 6/6 markers.
[2024-01-25 19:35:17,921] [INFO] Query marker FASTA was written to GCF_009469765.1_ASM946976v1_genomic.fna/markers.fasta
[2024-01-25 19:35:17,921] [INFO] Task started: Blastn
[2024-01-25 19:35:17,921] [INFO] Running command: blastn -query GCF_009469765.1_ASM946976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb809d9c-9c24-4666-92a6-4699ae4e5392/dqc_reference/reference_markers.fasta -out GCF_009469765.1_ASM946976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:18,781] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:18,784] [INFO] Selected 13 target genomes.
[2024-01-25 19:35:18,784] [INFO] Target genome list was writen to GCF_009469765.1_ASM946976v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:18,786] [INFO] Task started: fastANI
[2024-01-25 19:35:18,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgffc30622-a926-41a3-ad75-b00fc58da97a/GCF_009469765.1_ASM946976v1_genomic.fna.gz --refList GCF_009469765.1_ASM946976v1_genomic.fna/target_genomes.txt --output GCF_009469765.1_ASM946976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:29,379] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:29,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb809d9c-9c24-4666-92a6-4699ae4e5392/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:29,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb809d9c-9c24-4666-92a6-4699ae4e5392/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:29,388] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:29,389] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:29,389] [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
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	100.0	1410	1413	95	conclusive
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	94.5467	1211	1413	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	82.3372	690	1413	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	81.9987	638	1413	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.5474	365	1413	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.5471	430	1413	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	78.4796	449	1413	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	78.1613	305	1413	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.8389	255	1413	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.7599	224	1413	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	76.5365	230	1413	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	76.4133	167	1413	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	76.4096	185	1413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:29,391] [INFO] DFAST Taxonomy check result was written to GCF_009469765.1_ASM946976v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:29,391] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:29,392] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:29,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb809d9c-9c24-4666-92a6-4699ae4e5392/dqc_reference/checkm_data
[2024-01-25 19:35:29,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:29,433] [INFO] Task started: CheckM
[2024-01-25 19:35:29,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009469765.1_ASM946976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009469765.1_ASM946976v1_genomic.fna/checkm_input GCF_009469765.1_ASM946976v1_genomic.fna/checkm_result
[2024-01-25 19:36:03,988] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:03,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:04,018] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:04,019] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:04,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009469765.1_ASM946976v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:04,022] [INFO] Task started: Blastn
[2024-01-25 19:36:04,022] [INFO] Running command: blastn -query GCF_009469765.1_ASM946976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb809d9c-9c24-4666-92a6-4699ae4e5392/dqc_reference/reference_markers_gtdb.fasta -out GCF_009469765.1_ASM946976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:05,736] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:05,746] [INFO] Selected 16 target genomes.
[2024-01-25 19:36:05,746] [INFO] Target genome list was writen to GCF_009469765.1_ASM946976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:05,759] [INFO] Task started: fastANI
[2024-01-25 19:36:05,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgffc30622-a926-41a3-ad75-b00fc58da97a/GCF_009469765.1_ASM946976v1_genomic.fna.gz --refList GCF_009469765.1_ASM946976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009469765.1_ASM946976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:21,272] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:21,282] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:21,283] [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_009469765.1	s__Azonexus hortensis	100.0	1409	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001551835.1	s__Azonexus denitrificans	94.5479	1211	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440665.1	s__Azonexus sp002440665	83.5635	699	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275485.1	s__Azonexus sp012275485	83.4973	891	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469615.1	s__Azonexus sp009469615	83.4884	757	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983615.1	s__Azonexus sp017983615	83.1994	679	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003583745.1	s__Azonexus sp003583745	83.114	827	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828385.1	s__Azonexus sp018828385	82.9723	807	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	100.00	100.00	1.00	1.00	4	-
GCA_018261905.1	s__Azonexus sp018261905	82.7768	804	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840785.1	s__Azonexus sp002840785	82.7334	750	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	82.5848	702	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012425.1	s__Azonexus aromaticus_A	82.5695	815	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.34	97.34	0.89	0.89	2	-
GCA_013363835.1	s__Azonexus sp013363835	82.5638	686	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_907163225.1	s__Azonexus sp907163225	82.5623	689	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864195.1	s__Azonexus sp016864195	82.5531	722	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470165.1	s__Azonexus sp002470165	82.0477	450	1413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:21,286] [INFO] GTDB search result was written to GCF_009469765.1_ASM946976v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:21,286] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:21,289] [INFO] DFAST_QC result json was written to GCF_009469765.1_ASM946976v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:21,290] [INFO] DFAST_QC completed!
[2024-01-25 19:36:21,290] [INFO] Total running time: 0h1m16s