[2024-01-25 20:08:05,709] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:08:05,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:08:05,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg28d9852e-78aa-4c10-b7fc-63862a90719e/dqc_reference
[2024-01-25 20:08:06,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:08:06,889] [INFO] Task started: Prodigal
[2024-01-25 20:08:06,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg048fdf1d-5644-4f62-b97e-66272f80edd6/GCF_026072915.1_ASM2607291v1_genomic.fna.gz | prodigal -d GCF_026072915.1_ASM2607291v1_genomic.fna/cds.fna -a GCF_026072915.1_ASM2607291v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:23,380] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:23,380] [INFO] Task started: HMMsearch
[2024-01-25 20:08:23,380] [INFO] Running command: hmmsearch --tblout GCF_026072915.1_ASM2607291v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28d9852e-78aa-4c10-b7fc-63862a90719e/dqc_reference/reference_markers.hmm GCF_026072915.1_ASM2607291v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:23,583] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:23,584] [INFO] Found 6/6 markers.
[2024-01-25 20:08:23,608] [INFO] Query marker FASTA was written to GCF_026072915.1_ASM2607291v1_genomic.fna/markers.fasta
[2024-01-25 20:08:23,608] [INFO] Task started: Blastn
[2024-01-25 20:08:23,608] [INFO] Running command: blastn -query GCF_026072915.1_ASM2607291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28d9852e-78aa-4c10-b7fc-63862a90719e/dqc_reference/reference_markers.fasta -out GCF_026072915.1_ASM2607291v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:24,144] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:24,147] [INFO] Selected 11 target genomes.
[2024-01-25 20:08:24,147] [INFO] Target genome list was writen to GCF_026072915.1_ASM2607291v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:24,153] [INFO] Task started: fastANI
[2024-01-25 20:08:24,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg048fdf1d-5644-4f62-b97e-66272f80edd6/GCF_026072915.1_ASM2607291v1_genomic.fna.gz --refList GCF_026072915.1_ASM2607291v1_genomic.fna/target_genomes.txt --output GCF_026072915.1_ASM2607291v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:31,944] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:31,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28d9852e-78aa-4c10-b7fc-63862a90719e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:31,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28d9852e-78aa-4c10-b7fc-63862a90719e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:31,950] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:08:31,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:08:31,950] [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=DSM 22959	GCA_008000975.1	239935	239935	type	True	82.5628	650	1058	95	below_threshold
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_017504145.1	239935	239935	type	True	82.5405	653	1058	95	below_threshold
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_000020225.1	239935	239935	type	True	82.5252	651	1058	95	below_threshold
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	77.3954	145	1058	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	76.9075	54	1058	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.7518	64	1058	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:31,951] [INFO] DFAST Taxonomy check result was written to GCF_026072915.1_ASM2607291v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:31,952] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:31,952] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:31,952] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28d9852e-78aa-4c10-b7fc-63862a90719e/dqc_reference/checkm_data
[2024-01-25 20:08:31,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:31,985] [INFO] Task started: CheckM
[2024-01-25 20:08:31,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026072915.1_ASM2607291v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026072915.1_ASM2607291v1_genomic.fna/checkm_input GCF_026072915.1_ASM2607291v1_genomic.fna/checkm_result
[2024-01-25 20:09:17,179] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:17,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:17,195] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:17,195] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:17,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026072915.1_ASM2607291v1_genomic.fna/markers.fasta)
[2024-01-25 20:09:17,196] [INFO] Task started: Blastn
[2024-01-25 20:09:17,196] [INFO] Running command: blastn -query GCF_026072915.1_ASM2607291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28d9852e-78aa-4c10-b7fc-63862a90719e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026072915.1_ASM2607291v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:17,968] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:17,971] [INFO] Selected 6 target genomes.
[2024-01-25 20:09:17,971] [INFO] Target genome list was writen to GCF_026072915.1_ASM2607291v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:17,981] [INFO] Task started: fastANI
[2024-01-25 20:09:17,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg048fdf1d-5644-4f62-b97e-66272f80edd6/GCF_026072915.1_ASM2607291v1_genomic.fna.gz --refList GCF_026072915.1_ASM2607291v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026072915.1_ASM2607291v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:09:22,776] [INFO] Task succeeded: fastANI
[2024-01-25 20:09:22,780] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:09:22,781] [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_018847895.1	s__Akkermansia sp001580195	99.9733	1050	1058	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.22	96.77	0.98	0.92	18	conclusive
GCF_004167605.1	s__Akkermansia sp004167605	94.313	886	1058	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.95	99.06	0.99	0.93	74	-
GCF_018709685.1	s__Akkermansia muciniphila_E	84.6964	742	1058	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018847375.1	s__Akkermansia muciniphila_B	84.6132	792	1058	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	84.4544	760	1058	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.91	98.50	0.94	0.90	5	-
GCA_905200945.1	s__Akkermansia sp905200945	82.3052	649	1058	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:09:22,782] [INFO] GTDB search result was written to GCF_026072915.1_ASM2607291v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:09:22,782] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:09:22,784] [INFO] DFAST_QC result json was written to GCF_026072915.1_ASM2607291v1_genomic.fna/dqc_result.json
[2024-01-25 20:09:22,784] [INFO] DFAST_QC completed!
[2024-01-25 20:09:22,784] [INFO] Total running time: 0h1m17s