[2023-06-29 18:37:23,092] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:37:23,095] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:37:23,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ab051f8-f123-4501-a472-337fa575a56a/dqc_reference
[2023-06-29 18:37:24,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:37:24,576] [INFO] Task started: Prodigal
[2023-06-29 18:37:24,576] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bb772e6-3a47-4317-9d9a-32ace91533d3/GCA_021205065.1_ASM2120506v1_genomic.fna.gz | prodigal -d GCA_021205065.1_ASM2120506v1_genomic.fna/cds.fna -a GCA_021205065.1_ASM2120506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:37:39,730] [INFO] Task succeeded: Prodigal
[2023-06-29 18:37:39,731] [INFO] Task started: HMMsearch
[2023-06-29 18:37:39,731] [INFO] Running command: hmmsearch --tblout GCA_021205065.1_ASM2120506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ab051f8-f123-4501-a472-337fa575a56a/dqc_reference/reference_markers.hmm GCA_021205065.1_ASM2120506v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:37:40,031] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:37:40,032] [INFO] Found 6/6 markers.
[2023-06-29 18:37:40,061] [INFO] Query marker FASTA was written to GCA_021205065.1_ASM2120506v1_genomic.fna/markers.fasta
[2023-06-29 18:37:40,062] [INFO] Task started: Blastn
[2023-06-29 18:37:40,062] [INFO] Running command: blastn -query GCA_021205065.1_ASM2120506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ab051f8-f123-4501-a472-337fa575a56a/dqc_reference/reference_markers.fasta -out GCA_021205065.1_ASM2120506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:37:40,720] [INFO] Task succeeded: Blastn
[2023-06-29 18:37:40,724] [INFO] Selected 10 target genomes.
[2023-06-29 18:37:40,724] [INFO] Target genome list was writen to GCA_021205065.1_ASM2120506v1_genomic.fna/target_genomes.txt
[2023-06-29 18:37:40,725] [INFO] Task started: fastANI
[2023-06-29 18:37:40,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bb772e6-3a47-4317-9d9a-32ace91533d3/GCA_021205065.1_ASM2120506v1_genomic.fna.gz --refList GCA_021205065.1_ASM2120506v1_genomic.fna/target_genomes.txt --output GCA_021205065.1_ASM2120506v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:37:47,925] [INFO] Task succeeded: fastANI
[2023-06-29 18:37:47,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ab051f8-f123-4501-a472-337fa575a56a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:37:47,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ab051f8-f123-4501-a472-337fa575a56a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:37:47,935] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2023-06-29 18:37:47,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 18:37:47,936] [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
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_000020225.1	239935	239935	type	True	98.7504	727	765	95	conclusive
Akkermansia muciniphila	strain=DSM 22959	GCA_008000975.1	239935	239935	type	True	98.6969	732	765	95	conclusive
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_017504145.1	239935	239935	type	True	98.6653	734	765	95	conclusive
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	77.3351	95	765	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 18:37:47,942] [INFO] DFAST Taxonomy check result was written to GCA_021205065.1_ASM2120506v1_genomic.fna/tc_result.tsv
[2023-06-29 18:37:47,949] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:37:47,949] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:37:47,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ab051f8-f123-4501-a472-337fa575a56a/dqc_reference/checkm_data
[2023-06-29 18:37:47,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:37:47,985] [INFO] Task started: CheckM
[2023-06-29 18:37:47,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021205065.1_ASM2120506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021205065.1_ASM2120506v1_genomic.fna/checkm_input GCA_021205065.1_ASM2120506v1_genomic.fna/checkm_result
[2023-06-29 18:38:32,218] [INFO] Task succeeded: CheckM
[2023-06-29 18:38:32,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 18:38:32,244] [INFO] ===== Completeness check finished =====
[2023-06-29 18:38:32,244] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:38:32,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021205065.1_ASM2120506v1_genomic.fna/markers.fasta)
[2023-06-29 18:38:32,245] [INFO] Task started: Blastn
[2023-06-29 18:38:32,246] [INFO] Running command: blastn -query GCA_021205065.1_ASM2120506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ab051f8-f123-4501-a472-337fa575a56a/dqc_reference/reference_markers_gtdb.fasta -out GCA_021205065.1_ASM2120506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:38:33,062] [INFO] Task succeeded: Blastn
[2023-06-29 18:38:33,067] [INFO] Selected 11 target genomes.
[2023-06-29 18:38:33,067] [INFO] Target genome list was writen to GCA_021205065.1_ASM2120506v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:38:33,070] [INFO] Task started: fastANI
[2023-06-29 18:38:33,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bb772e6-3a47-4317-9d9a-32ace91533d3/GCA_021205065.1_ASM2120506v1_genomic.fna.gz --refList GCA_021205065.1_ASM2120506v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021205065.1_ASM2120506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:38:40,061] [INFO] Task succeeded: fastANI
[2023-06-29 18:38:40,075] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:38:40,075] [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_000020225.1	s__Akkermansia muciniphila	98.7504	727	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.03	97.15	0.94	0.85	200	conclusive
GCA_905200945.1	s__Akkermansia sp905200945	94.656	711	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184965.1	s__Akkermansia muciniphila_A	93.8243	686	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.74	97.99	0.96	0.93	10	-
GCF_018847375.1	s__Akkermansia muciniphila_B	87.4373	670	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.85	95.28	0.95	0.86	44	-
GCF_002884975.1	s__Akkermansia muciniphila_C	85.8791	663	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.91	98.50	0.94	0.90	5	-
GCF_018709685.1	s__Akkermansia muciniphila_E	85.7944	634	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018847895.1	s__Akkermansia sp001580195	82.3972	594	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.22	96.77	0.98	0.92	18	-
--------------------------------------------------------------------------------
[2023-06-29 18:38:40,078] [INFO] GTDB search result was written to GCA_021205065.1_ASM2120506v1_genomic.fna/result_gtdb.tsv
[2023-06-29 18:38:40,078] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:38:40,081] [INFO] DFAST_QC result json was written to GCA_021205065.1_ASM2120506v1_genomic.fna/dqc_result.json
[2023-06-29 18:38:40,081] [INFO] DFAST_QC completed!
[2023-06-29 18:38:40,081] [INFO] Total running time: 0h1m17s