[2024-01-25 19:50:50,617] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:50,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:50,618] [INFO] DQC Reference Directory: /var/lib/cwl/stgd08b3193-3e07-4c48-94c0-e52848941f91/dqc_reference
[2024-01-25 19:50:51,744] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:51,745] [INFO] Task started: Prodigal
[2024-01-25 19:50:51,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e49522e-c127-4a79-b304-3ade8f34171b/GCF_010681825.2_ASM1068182v2_genomic.fna.gz | prodigal -d GCF_010681825.2_ASM1068182v2_genomic.fna/cds.fna -a GCF_010681825.2_ASM1068182v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:17,461] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:17,461] [INFO] Task started: HMMsearch
[2024-01-25 19:51:17,461] [INFO] Running command: hmmsearch --tblout GCF_010681825.2_ASM1068182v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd08b3193-3e07-4c48-94c0-e52848941f91/dqc_reference/reference_markers.hmm GCF_010681825.2_ASM1068182v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:17,674] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:17,675] [INFO] Found 6/6 markers.
[2024-01-25 19:51:17,704] [INFO] Query marker FASTA was written to GCF_010681825.2_ASM1068182v2_genomic.fna/markers.fasta
[2024-01-25 19:51:17,704] [INFO] Task started: Blastn
[2024-01-25 19:51:17,704] [INFO] Running command: blastn -query GCF_010681825.2_ASM1068182v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd08b3193-3e07-4c48-94c0-e52848941f91/dqc_reference/reference_markers.fasta -out GCF_010681825.2_ASM1068182v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:18,263] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:18,266] [INFO] Selected 22 target genomes.
[2024-01-25 19:51:18,266] [INFO] Target genome list was writen to GCF_010681825.2_ASM1068182v2_genomic.fna/target_genomes.txt
[2024-01-25 19:51:18,284] [INFO] Task started: fastANI
[2024-01-25 19:51:18,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e49522e-c127-4a79-b304-3ade8f34171b/GCF_010681825.2_ASM1068182v2_genomic.fna.gz --refList GCF_010681825.2_ASM1068182v2_genomic.fna/target_genomes.txt --output GCF_010681825.2_ASM1068182v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:35,945] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:35,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd08b3193-3e07-4c48-94c0-e52848941f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:35,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd08b3193-3e07-4c48-94c0-e52848941f91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:35,951] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:35,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:35,951] [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
Sulfuriroseicoccus oceanibius	strain=T37	GCA_010681825.2	2707525	2707525	type	True	100.0	1164	1165	95	conclusive
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	77.3014	53	1165	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	77.0853	65	1165	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.9906	88	1165	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.835	68	1165	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	76.4601	54	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:35,953] [INFO] DFAST Taxonomy check result was written to GCF_010681825.2_ASM1068182v2_genomic.fna/tc_result.tsv
[2024-01-25 19:51:35,953] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:35,953] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:35,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd08b3193-3e07-4c48-94c0-e52848941f91/dqc_reference/checkm_data
[2024-01-25 19:51:35,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:35,990] [INFO] Task started: CheckM
[2024-01-25 19:51:35,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010681825.2_ASM1068182v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010681825.2_ASM1068182v2_genomic.fna/checkm_input GCF_010681825.2_ASM1068182v2_genomic.fna/checkm_result
[2024-01-25 19:52:48,162] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:48,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:48,183] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:48,183] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:48,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010681825.2_ASM1068182v2_genomic.fna/markers.fasta)
[2024-01-25 19:52:48,184] [INFO] Task started: Blastn
[2024-01-25 19:52:48,184] [INFO] Running command: blastn -query GCF_010681825.2_ASM1068182v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd08b3193-3e07-4c48-94c0-e52848941f91/dqc_reference/reference_markers_gtdb.fasta -out GCF_010681825.2_ASM1068182v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:49,076] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:49,078] [INFO] Selected 23 target genomes.
[2024-01-25 19:52:49,078] [INFO] Target genome list was writen to GCF_010681825.2_ASM1068182v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:49,121] [INFO] Task started: fastANI
[2024-01-25 19:52:49,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e49522e-c127-4a79-b304-3ade8f34171b/GCF_010681825.2_ASM1068182v2_genomic.fna.gz --refList GCF_010681825.2_ASM1068182v2_genomic.fna/target_genomes_gtdb.txt --output GCF_010681825.2_ASM1068182v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:07,686] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:07,692] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:07,693] [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_010681825.2	s__JAAGVW01 sp010681825	100.0	1164	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__SLCJ01;g__JAAGVW01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018137965.1	s__Luteolibacter sp018137965	77.0243	89	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	76.843	68	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016811075.1	s__UBA985 sp016811075	76.8213	57	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__UBA985	95.0	99.37	98.74	0.97	0.95	3	-
GCA_002304315.1	s__Haloferula sp002304315	76.4648	65	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003820635.1	s__Luteolibacter sp003820635	76.2445	67	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	76.0991	59	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126655.1	s__Luteolibacter sp007126655	76.0226	59	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.62	99.62	0.82	0.82	2	-
GCA_017301995.1	s__Luteolibacter sp017301995	75.4634	50	1165	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:07,696] [INFO] GTDB search result was written to GCF_010681825.2_ASM1068182v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:07,702] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:07,704] [INFO] DFAST_QC result json was written to GCF_010681825.2_ASM1068182v2_genomic.fna/dqc_result.json
[2024-01-25 19:53:07,704] [INFO] DFAST_QC completed!
[2024-01-25 19:53:07,704] [INFO] Total running time: 0h2m17s