[2024-01-24 13:18:26,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b6b6331-58a3-46d1-8c50-57e0dccdeba0/dqc_reference
[2024-01-24 13:18:27,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,412] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,412] [INFO] Running command: gunzip -c /var/lib/cwl/stg64706653-05a9-4e36-85cb-3874da7a24b6/GCF_028874535.1_ASM2887453v1_genomic.fna.gz | prodigal -d GCF_028874535.1_ASM2887453v1_genomic.fna/cds.fna -a GCF_028874535.1_ASM2887453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:36,418] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:36,418] [INFO] Task started: HMMsearch
[2024-01-24 13:18:36,419] [INFO] Running command: hmmsearch --tblout GCF_028874535.1_ASM2887453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b6b6331-58a3-46d1-8c50-57e0dccdeba0/dqc_reference/reference_markers.hmm GCF_028874535.1_ASM2887453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:36,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:36,630] [INFO] Found 6/6 markers.
[2024-01-24 13:18:36,694] [INFO] Query marker FASTA was written to GCF_028874535.1_ASM2887453v1_genomic.fna/markers.fasta
[2024-01-24 13:18:36,694] [INFO] Task started: Blastn
[2024-01-24 13:18:36,694] [INFO] Running command: blastn -query GCF_028874535.1_ASM2887453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b6b6331-58a3-46d1-8c50-57e0dccdeba0/dqc_reference/reference_markers.fasta -out GCF_028874535.1_ASM2887453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:37,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:37,335] [INFO] Selected 22 target genomes.
[2024-01-24 13:18:37,335] [INFO] Target genome list was writen to GCF_028874535.1_ASM2887453v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:37,343] [INFO] Task started: fastANI
[2024-01-24 13:18:37,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg64706653-05a9-4e36-85cb-3874da7a24b6/GCF_028874535.1_ASM2887453v1_genomic.fna.gz --refList GCF_028874535.1_ASM2887453v1_genomic.fna/target_genomes.txt --output GCF_028874535.1_ASM2887453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:54,791] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:54,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b6b6331-58a3-46d1-8c50-57e0dccdeba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:54,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b6b6331-58a3-46d1-8c50-57e0dccdeba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:54,803] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:54,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:54,803] [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
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	74.9336	101	1133	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	74.893	98	1133	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	74.8884	99	1133	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	74.8504	53	1133	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	74.8504	53	1133	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8484	99	1133	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	74.7501	91	1133	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	74.723	77	1133	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.7092	93	1133	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	74.7015	86	1133	95	below_threshold
Halorubrum halodurans	strain=Cb34	GCA_002252985.1	1383851	1383851	type	True	74.6414	61	1133	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	74.6351	64	1133	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	74.5233	57	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:54,806] [INFO] DFAST Taxonomy check result was written to GCF_028874535.1_ASM2887453v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:54,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:54,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:54,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b6b6331-58a3-46d1-8c50-57e0dccdeba0/dqc_reference/checkm_data
[2024-01-24 13:18:54,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:54,846] [INFO] Task started: CheckM
[2024-01-24 13:18:54,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028874535.1_ASM2887453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028874535.1_ASM2887453v1_genomic.fna/checkm_input GCF_028874535.1_ASM2887453v1_genomic.fna/checkm_result
[2024-01-24 13:19:27,646] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:27,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:27,678] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:27,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:27,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028874535.1_ASM2887453v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:27,678] [INFO] Task started: Blastn
[2024-01-24 13:19:27,679] [INFO] Running command: blastn -query GCF_028874535.1_ASM2887453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b6b6331-58a3-46d1-8c50-57e0dccdeba0/dqc_reference/reference_markers_gtdb.fasta -out GCF_028874535.1_ASM2887453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:28,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:28,701] [INFO] Selected 5 target genomes.
[2024-01-24 13:19:28,701] [INFO] Target genome list was writen to GCF_028874535.1_ASM2887453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:28,708] [INFO] Task started: fastANI
[2024-01-24 13:19:28,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg64706653-05a9-4e36-85cb-3874da7a24b6/GCF_028874535.1_ASM2887453v1_genomic.fna.gz --refList GCF_028874535.1_ASM2887453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028874535.1_ASM2887453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:33,294] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:33,300] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:33,300] [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
GCA_009840115.1	s__JAAXHJ01 sp009840115	92.1627	961	1133	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	99.91	99.91	0.95	0.95	2	-
GCA_009841015.1	s__JAAXHJ01 sp009841015	90.6125	896	1133	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841005.1	s__JAAXHJ01 sp009841005	90.563	839	1133	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	96.67	96.60	0.84	0.81	5	-
GCA_009838765.1	s__JAAXHJ01 sp009838765	90.2261	916	1133	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	99.96	99.96	0.97	0.96	3	-
GCA_012270965.1	s__JAAXHJ01 sp012270965	89.2384	872	1133	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__JABDQB01;g__JAAXHJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:33,301] [INFO] GTDB search result was written to GCF_028874535.1_ASM2887453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:33,302] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:33,305] [INFO] DFAST_QC result json was written to GCF_028874535.1_ASM2887453v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:33,305] [INFO] DFAST_QC completed!
[2024-01-24 13:19:33,305] [INFO] Total running time: 0h1m7s