[2023-06-19 14:48:54,649] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:48:54,652] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:48:54,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg416d2117-d050-4f51-b06f-7d46b253308f/dqc_reference
[2023-06-19 14:48:56,019] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:48:56,020] [INFO] Task started: Prodigal
[2023-06-19 14:48:56,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg61b957d2-efd3-4218-9261-0c5ff5b39935/GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:49:13,022] [INFO] Task succeeded: Prodigal
[2023-06-19 14:49:13,023] [INFO] Task started: HMMsearch
[2023-06-19 14:49:13,023] [INFO] Running command: hmmsearch --tblout GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg416d2117-d050-4f51-b06f-7d46b253308f/dqc_reference/reference_markers.hmm GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:49:13,264] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:49:13,265] [INFO] Found 6/6 markers.
[2023-06-19 14:49:13,298] [INFO] Query marker FASTA was written to GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 14:49:13,299] [INFO] Task started: Blastn
[2023-06-19 14:49:13,299] [INFO] Running command: blastn -query GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg416d2117-d050-4f51-b06f-7d46b253308f/dqc_reference/reference_markers.fasta -out GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:49:14,832] [INFO] Task succeeded: Blastn
[2023-06-19 14:49:14,837] [INFO] Selected 9 target genomes.
[2023-06-19 14:49:14,838] [INFO] Target genome list was writen to GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 14:49:14,867] [INFO] Task started: fastANI
[2023-06-19 14:49:14,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg61b957d2-efd3-4218-9261-0c5ff5b39935/GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:49:21,829] [INFO] Task succeeded: fastANI
[2023-06-19 14:49:21,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg416d2117-d050-4f51-b06f-7d46b253308f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:49:21,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg416d2117-d050-4f51-b06f-7d46b253308f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:49:21,837] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2023-06-19 14:49:21,837] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 14:49:21,837] [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_017504145.1	239935	239935	type	True	96.5757	798	895	95	conclusive
Akkermansia muciniphila	strain=DSM 22959	GCA_008000975.1	239935	239935	type	True	96.5654	801	895	95	conclusive
Akkermansia muciniphila	strain=ATCC BAA-835	GCA_000020225.1	239935	239935	type	True	96.5547	810	895	95	conclusive
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	77.1507	95	895	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:49:21,840] [INFO] DFAST Taxonomy check result was written to GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 14:49:21,842] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:49:21,842] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:49:21,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg416d2117-d050-4f51-b06f-7d46b253308f/dqc_reference/checkm_data
[2023-06-19 14:49:21,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:49:21,880] [INFO] Task started: CheckM
[2023-06-19 14:49:21,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 14:50:10,881] [INFO] Task succeeded: CheckM
[2023-06-19 14:50:10,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:50:10,910] [INFO] ===== Completeness check finished =====
[2023-06-19 14:50:10,910] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:50:10,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 14:50:10,911] [INFO] Task started: Blastn
[2023-06-19 14:50:10,911] [INFO] Running command: blastn -query GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg416d2117-d050-4f51-b06f-7d46b253308f/dqc_reference/reference_markers_gtdb.fasta -out GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:50:11,702] [INFO] Task succeeded: Blastn
[2023-06-19 14:50:11,708] [INFO] Selected 7 target genomes.
[2023-06-19 14:50:11,708] [INFO] Target genome list was writen to GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:50:11,731] [INFO] Task started: fastANI
[2023-06-19 14:50:11,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg61b957d2-efd3-4218-9261-0c5ff5b39935/GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:50:16,787] [INFO] Task succeeded: fastANI
[2023-06-19 14:50:16,802] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:50:16,802] [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	96.5646	809	895	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	94.6025	795	895	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	94.5726	778	895	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	87.4284	732	895	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	85.8015	714	895	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	85.6939	696	895	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	82.4576	640	895	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	99.22	96.77	0.98	0.92	18	-
--------------------------------------------------------------------------------
[2023-06-19 14:50:16,805] [INFO] GTDB search result was written to GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 14:50:16,806] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:50:16,809] [INFO] DFAST_QC result json was written to GCA_937925975.1_ERR1190960_bin.2_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 14:50:16,810] [INFO] DFAST_QC completed!
[2023-06-19 14:50:16,810] [INFO] Total running time: 0h1m22s