[2024-01-24 14:05:36,718] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg383796e8-9681-4ba9-8811-258957506952/dqc_reference
[2024-01-24 14:05:38,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:38,152] [INFO] Task started: Prodigal
[2024-01-24 14:05:38,152] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfcf7272-2fbb-431a-91b5-9a92f9e4c04a/GCF_013868155.1_ASM1386815v1_genomic.fna.gz | prodigal -d GCF_013868155.1_ASM1386815v1_genomic.fna/cds.fna -a GCF_013868155.1_ASM1386815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:48,217] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:48,217] [INFO] Task started: HMMsearch
[2024-01-24 14:05:48,217] [INFO] Running command: hmmsearch --tblout GCF_013868155.1_ASM1386815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg383796e8-9681-4ba9-8811-258957506952/dqc_reference/reference_markers.hmm GCF_013868155.1_ASM1386815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:48,513] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:48,514] [INFO] Found 6/6 markers.
[2024-01-24 14:05:48,571] [INFO] Query marker FASTA was written to GCF_013868155.1_ASM1386815v1_genomic.fna/markers.fasta
[2024-01-24 14:05:48,572] [INFO] Task started: Blastn
[2024-01-24 14:05:48,572] [INFO] Running command: blastn -query GCF_013868155.1_ASM1386815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg383796e8-9681-4ba9-8811-258957506952/dqc_reference/reference_markers.fasta -out GCF_013868155.1_ASM1386815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:49,939] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:49,942] [INFO] Selected 14 target genomes.
[2024-01-24 14:05:49,942] [INFO] Target genome list was writen to GCF_013868155.1_ASM1386815v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:49,948] [INFO] Task started: fastANI
[2024-01-24 14:05:49,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfcf7272-2fbb-431a-91b5-9a92f9e4c04a/GCF_013868155.1_ASM1386815v1_genomic.fna.gz --refList GCF_013868155.1_ASM1386815v1_genomic.fna/target_genomes.txt --output GCF_013868155.1_ASM1386815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:01,724] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:01,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg383796e8-9681-4ba9-8811-258957506952/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:01,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg383796e8-9681-4ba9-8811-258957506952/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:01,736] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:01,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:01,737] [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
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	100.0	1089	1089	95	conclusive
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	93.6719	983	1089	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	88.1232	919	1089	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	88.0924	919	1089	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	80.8378	542	1089	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	80.4835	532	1089	95	below_threshold
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	80.3284	523	1089	95	below_threshold
Aeromicrobium camelliae	strain=YS17T	GCA_003850045.1	1538144	1538144	type	True	80.2238	488	1089	95	below_threshold
Aeromicrobium phragmitis	strain=9W16Y-2	GCA_003674095.1	2478914	2478914	type	True	80.0289	470	1089	95	below_threshold
Aeromicrobium piscarium	strain=Co35	GCA_007421815.1	2590901	2590901	type	True	79.919	452	1089	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	78.6851	400	1089	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	78.4498	381	1089	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	78.3878	401	1089	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	78.0715	403	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:01,738] [INFO] DFAST Taxonomy check result was written to GCF_013868155.1_ASM1386815v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:01,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:01,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:01,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg383796e8-9681-4ba9-8811-258957506952/dqc_reference/checkm_data
[2024-01-24 14:06:01,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:01,777] [INFO] Task started: CheckM
[2024-01-24 14:06:01,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013868155.1_ASM1386815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013868155.1_ASM1386815v1_genomic.fna/checkm_input GCF_013868155.1_ASM1386815v1_genomic.fna/checkm_result
[2024-01-24 14:06:57,201] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:57,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:57,223] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:57,223] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:57,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013868155.1_ASM1386815v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:57,224] [INFO] Task started: Blastn
[2024-01-24 14:06:57,224] [INFO] Running command: blastn -query GCF_013868155.1_ASM1386815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg383796e8-9681-4ba9-8811-258957506952/dqc_reference/reference_markers_gtdb.fasta -out GCF_013868155.1_ASM1386815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:59,456] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:59,460] [INFO] Selected 5 target genomes.
[2024-01-24 14:06:59,460] [INFO] Target genome list was writen to GCF_013868155.1_ASM1386815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:59,467] [INFO] Task started: fastANI
[2024-01-24 14:06:59,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfcf7272-2fbb-431a-91b5-9a92f9e4c04a/GCF_013868155.1_ASM1386815v1_genomic.fna.gz --refList GCF_013868155.1_ASM1386815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013868155.1_ASM1386815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:04,050] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:04,055] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:04,055] [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_013868155.1	s__Aeromicrobium phoceense	100.0	1089	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.64	97.64	0.92	0.92	2	conclusive
GCF_900167475.1	s__Aeromicrobium choanae	93.6719	983	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408555.1	s__Aeromicrobium tamlense	88.1083	920	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007992115.1	s__Aeromicrobium flavum	86.8809	791	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334735.1	s__Aeromicrobium sp014334735	85.6917	819	1089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	99.41	98.82	0.96	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:04,057] [INFO] GTDB search result was written to GCF_013868155.1_ASM1386815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:04,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:04,061] [INFO] DFAST_QC result json was written to GCF_013868155.1_ASM1386815v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:04,061] [INFO] DFAST_QC completed!
[2024-01-24 14:07:04,061] [INFO] Total running time: 0h1m27s