[2024-01-24 14:31:29,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:29,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:29,940] [INFO] DQC Reference Directory: /var/lib/cwl/stge2cdf421-6d5b-42ef-a7e1-09bb66e1420c/dqc_reference
[2024-01-24 14:31:31,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:31,336] [INFO] Task started: Prodigal
[2024-01-24 14:31:31,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg93bd231f-bd58-4ae5-8d22-1ee86ce33666/GCF_001683795.1_ASM168379v1_genomic.fna.gz | prodigal -d GCF_001683795.1_ASM168379v1_genomic.fna/cds.fna -a GCF_001683795.1_ASM168379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:53,314] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:53,314] [INFO] Task started: HMMsearch
[2024-01-24 14:31:53,315] [INFO] Running command: hmmsearch --tblout GCF_001683795.1_ASM168379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2cdf421-6d5b-42ef-a7e1-09bb66e1420c/dqc_reference/reference_markers.hmm GCF_001683795.1_ASM168379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:53,593] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:53,594] [INFO] Found 6/6 markers.
[2024-01-24 14:31:53,623] [INFO] Query marker FASTA was written to GCF_001683795.1_ASM168379v1_genomic.fna/markers.fasta
[2024-01-24 14:31:53,623] [INFO] Task started: Blastn
[2024-01-24 14:31:53,623] [INFO] Running command: blastn -query GCF_001683795.1_ASM168379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2cdf421-6d5b-42ef-a7e1-09bb66e1420c/dqc_reference/reference_markers.fasta -out GCF_001683795.1_ASM168379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:54,241] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:54,246] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:54,247] [INFO] Target genome list was writen to GCF_001683795.1_ASM168379v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:54,254] [INFO] Task started: fastANI
[2024-01-24 14:31:54,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg93bd231f-bd58-4ae5-8d22-1ee86ce33666/GCF_001683795.1_ASM168379v1_genomic.fna.gz --refList GCF_001683795.1_ASM168379v1_genomic.fna/target_genomes.txt --output GCF_001683795.1_ASM168379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:08,167] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:08,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2cdf421-6d5b-42ef-a7e1-09bb66e1420c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:08,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2cdf421-6d5b-42ef-a7e1-09bb66e1420c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:08,177] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:32:08,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:08,177] [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 glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	100.0	1005	1032	95	conclusive
Akkermansia muciniphila	strain=DSM 22959	GCA_008000975.1	239935	239935	type	True	77.0218	110	1032	95	below_threshold
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_017504145.1	239935	239935	type	True	77.0118	112	1032	95	below_threshold
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_000020225.1	239935	239935	type	True	76.9796	114	1032	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.3372	54	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:08,180] [INFO] DFAST Taxonomy check result was written to GCF_001683795.1_ASM168379v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:08,182] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:08,182] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:08,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2cdf421-6d5b-42ef-a7e1-09bb66e1420c/dqc_reference/checkm_data
[2024-01-24 14:32:08,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:08,225] [INFO] Task started: CheckM
[2024-01-24 14:32:08,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001683795.1_ASM168379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001683795.1_ASM168379v1_genomic.fna/checkm_input GCF_001683795.1_ASM168379v1_genomic.fna/checkm_result
[2024-01-24 14:33:08,538] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:08,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:08,562] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:08,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:08,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001683795.1_ASM168379v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:08,564] [INFO] Task started: Blastn
[2024-01-24 14:33:08,564] [INFO] Running command: blastn -query GCF_001683795.1_ASM168379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2cdf421-6d5b-42ef-a7e1-09bb66e1420c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001683795.1_ASM168379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:09,494] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:09,498] [INFO] Selected 20 target genomes.
[2024-01-24 14:33:09,498] [INFO] Target genome list was writen to GCF_001683795.1_ASM168379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:09,537] [INFO] Task started: fastANI
[2024-01-24 14:33:09,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg93bd231f-bd58-4ae5-8d22-1ee86ce33666/GCF_001683795.1_ASM168379v1_genomic.fna.gz --refList GCF_001683795.1_ASM168379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001683795.1_ASM168379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:18,186] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:18,210] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:18,210] [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_001683795.1	s__Akkermansia glycaniphila	100.0	1002	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.15	98.30	0.92	0.89	3	conclusive
GCF_004167605.1	s__Akkermansia sp004167605	77.7484	126	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.95	99.06	0.99	0.93	74	-
GCF_018847375.1	s__Akkermansia muciniphila_B	77.7003	133	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.85	95.28	0.95	0.86	44	-
GCA_900548895.1	s__Akkermansia intestinavium	77.6396	115	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.50	98.44	0.87	0.84	5	-
GCF_018709685.1	s__Akkermansia muciniphila_E	77.6174	124	1032	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	77.6164	131	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.22	96.77	0.98	0.92	18	-
GCF_002884975.1	s__Akkermansia muciniphila_C	77.4699	128	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.91	98.50	0.94	0.90	5	-
GCA_900545155.1	s__Akkermansia sp900545155	77.1927	95	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.52	99.06	0.96	0.94	3	-
GCA_905200945.1	s__Akkermansia sp905200945	77.1601	104	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015061985.1	s__Akkermansia sp015061985	76.9533	64	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.01	98.01	0.81	0.81	2	-
GCA_017379255.1	s__Akkermansia sp017379255	76.9513	73	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435365.1	s__Akkermansia sp017435365	76.9079	96	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937215.1	s__Akkermansia sp017937215	76.706	87	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	97.30	97.14	0.82	0.81	3	-
GCA_017546445.1	s__Akkermansia sp017546445	76.6123	83	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:18,212] [INFO] GTDB search result was written to GCF_001683795.1_ASM168379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:18,213] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:18,216] [INFO] DFAST_QC result json was written to GCF_001683795.1_ASM168379v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:18,216] [INFO] DFAST_QC completed!
[2024-01-24 14:33:18,216] [INFO] Total running time: 0h1m48s