[2023-06-13 14:45:07,105] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:45:07,107] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:45:07,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b97194f-ece4-4d37-848c-5e4356c981f1/dqc_reference
[2023-06-13 14:45:08,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:45:08,482] [INFO] Task started: Prodigal
[2023-06-13 14:45:08,482] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9ff797d-be65-45f1-bc41-25decfc1874b/GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:45:18,491] [INFO] Task succeeded: Prodigal
[2023-06-13 14:45:18,492] [INFO] Task started: HMMsearch
[2023-06-13 14:45:18,492] [INFO] Running command: hmmsearch --tblout GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b97194f-ece4-4d37-848c-5e4356c981f1/dqc_reference/reference_markers.hmm GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:45:18,658] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:45:18,660] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb9ff797d-be65-45f1-bc41-25decfc1874b/GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-13 14:45:18,678] [INFO] Query marker FASTA was written to GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 14:45:18,678] [INFO] Task started: Blastn
[2023-06-13 14:45:18,678] [INFO] Running command: blastn -query GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b97194f-ece4-4d37-848c-5e4356c981f1/dqc_reference/reference_markers.fasta -out GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:19,308] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:19,312] [INFO] Selected 16 target genomes.
[2023-06-13 14:45:19,312] [INFO] Target genome list was writen to GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 14:45:19,316] [INFO] Task started: fastANI
[2023-06-13 14:45:19,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9ff797d-be65-45f1-bc41-25decfc1874b/GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:45:28,883] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:28,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b97194f-ece4-4d37-848c-5e4356c981f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:45:28,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b97194f-ece4-4d37-848c-5e4356c981f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:45:28,887] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:45:28,887] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:45:28,887] [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	77.8493	76	510	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:45:28,889] [INFO] DFAST Taxonomy check result was written to GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 14:45:28,890] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:45:28,890] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:45:28,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b97194f-ece4-4d37-848c-5e4356c981f1/dqc_reference/checkm_data
[2023-06-13 14:45:28,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:45:28,914] [INFO] Task started: CheckM
[2023-06-13 14:45:28,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 14:46:01,034] [INFO] Task succeeded: CheckM
[2023-06-13 14:46:01,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:46:01,053] [INFO] ===== Completeness check finished =====
[2023-06-13 14:46:01,053] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:46:01,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 14:46:01,054] [INFO] Task started: Blastn
[2023-06-13 14:46:01,054] [INFO] Running command: blastn -query GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b97194f-ece4-4d37-848c-5e4356c981f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:46:02,104] [INFO] Task succeeded: Blastn
[2023-06-13 14:46:02,108] [INFO] Selected 13 target genomes.
[2023-06-13 14:46:02,108] [INFO] Target genome list was writen to GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:46:02,112] [INFO] Task started: fastANI
[2023-06-13 14:46:02,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9ff797d-be65-45f1-bc41-25decfc1874b/GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:46:06,835] [INFO] Task succeeded: fastANI
[2023-06-13 14:46:06,846] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:46:06,847] [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_900548895.1	s__Akkermansia intestinavium	98.4387	439	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.50	98.44	0.87	0.84	5	conclusive
GCA_019114365.1	s__Akkermansia intestinigallinarum	82.9976	322	510	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	79.0139	152	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409465.1	s__Akkermansia sp017409465	78.8228	113	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557455.1	s__Akkermansia muciniphila_D	78.7638	150	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	97.02	97.00	0.87	0.87	3	-
GCA_017937215.1	s__Akkermansia sp017937215	78.6551	157	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	97.30	97.14	0.82	0.81	3	-
GCA_017555465.1	s__Akkermansia sp017555465	78.5959	108	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017477935.1	s__Akkermansia sp017477935	78.5122	114	510	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	78.4607	121	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.01	98.01	0.81	0.81	2	-
GCA_017472085.1	s__Akkermansia sp017472085	78.1085	128	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017546845.1	s__Akkermansia sp017546845	77.9865	113	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017517805.1	s__Akkermansia sp017517805	77.9148	111	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521145.1	s__Akkermansia sp017521145	77.9018	104	510	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:46:06,849] [INFO] GTDB search result was written to GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 14:46:06,849] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:46:06,852] [INFO] DFAST_QC result json was written to GCA_907173335.1_ERR1543788_bin.1_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 14:46:06,852] [INFO] DFAST_QC completed!
[2023-06-13 14:46:06,852] [INFO] Total running time: 0h0m60s