[2023-06-13 15:45:17,435] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:45:17,440] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:45:17,440] [INFO] DQC Reference Directory: /var/lib/cwl/stgba7c4b9b-c8a9-42cd-bc4e-e83d8b19676b/dqc_reference
[2023-06-13 15:45:18,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:45:18,831] [INFO] Task started: Prodigal
[2023-06-13 15:45:18,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg62a95fc0-aaa2-4caa-9a23-da5297873dc2/GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:28,963] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:28,964] [INFO] Task started: HMMsearch
[2023-06-13 15:45:28,964] [INFO] Running command: hmmsearch --tblout GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba7c4b9b-c8a9-42cd-bc4e-e83d8b19676b/dqc_reference/reference_markers.hmm GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:29,139] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:29,140] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg62a95fc0-aaa2-4caa-9a23-da5297873dc2/GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 15:45:29,163] [INFO] Query marker FASTA was written to GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 15:45:29,163] [INFO] Task started: Blastn
[2023-06-13 15:45:29,163] [INFO] Running command: blastn -query GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgba7c4b9b-c8a9-42cd-bc4e-e83d8b19676b/dqc_reference/reference_markers.fasta -out GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:29,616] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:29,620] [INFO] Selected 5 target genomes.
[2023-06-13 15:45:29,620] [INFO] Target genome list was writen to GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 15:45:29,621] [INFO] Task started: fastANI
[2023-06-13 15:45:29,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg62a95fc0-aaa2-4caa-9a23-da5297873dc2/GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:33,718] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:33,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba7c4b9b-c8a9-42cd-bc4e-e83d8b19676b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:33,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba7c4b9b-c8a9-42cd-bc4e-e83d8b19676b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:33,724] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2023-06-13 15:45:33,724] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-13 15:45:33,725] [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
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	98.7044	535	736	95	inconclusive
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	98.6118	539	736	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_000156075.1	357276	357276	type	True	95.345	513	736	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	95.329	518	736	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	95.2854	519	736	95	inconclusive
--------------------------------------------------------------------------------
[2023-06-13 15:45:33,727] [INFO] DFAST Taxonomy check result was written to GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 15:45:33,727] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:33,728] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:33,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba7c4b9b-c8a9-42cd-bc4e-e83d8b19676b/dqc_reference/checkm_data
[2023-06-13 15:45:33,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:33,755] [INFO] Task started: CheckM
[2023-06-13 15:45:33,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 15:46:05,023] [INFO] Task succeeded: CheckM
[2023-06-13 15:46:05,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 20.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:46:05,042] [INFO] ===== Completeness check finished =====
[2023-06-13 15:46:05,042] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:46:05,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 15:46:05,042] [INFO] Task started: Blastn
[2023-06-13 15:46:05,042] [INFO] Running command: blastn -query GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgba7c4b9b-c8a9-42cd-bc4e-e83d8b19676b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:46:05,477] [INFO] Task succeeded: Blastn
[2023-06-13 15:46:05,481] [INFO] Selected 6 target genomes.
[2023-06-13 15:46:05,481] [INFO] Target genome list was writen to GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:46:05,482] [INFO] Task started: fastANI
[2023-06-13 15:46:05,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg62a95fc0-aaa2-4caa-9a23-da5297873dc2/GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:10,532] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:10,539] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:46:10,539] [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_000012825.1	s__Phocaeicola vulgatus	98.6486	538	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	98.84	95.43	0.81	0.61	263	conclusive
GCF_013009555.1	s__Phocaeicola dorei	95.329	518	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	99.04	97.27	0.84	0.54	104	-
GCF_000614185.1	s__Phocaeicola sartorii	90.5424	450	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	-
GCA_011959205.1	s__Phocaeicola sp011959205	90.1399	332	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.90	0.90	2	-
GCF_000382445.1	s__Phocaeicola massiliensis	81.2804	269	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.84	98.03	0.86	0.62	25	-
GCA_902388365.1	s__Phocaeicola sp902388365	80.8951	338	736	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.75	97.52	0.90	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:10,540] [INFO] GTDB search result was written to GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:10,541] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:10,544] [INFO] DFAST_QC result json was written to GCA_947039405.1_ERR8099099_bin.28_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 15:46:10,544] [INFO] DFAST_QC completed!
[2023-06-13 15:46:10,544] [INFO] Total running time: 0h0m53s