[2023-06-13 00:09:47,359] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:09:47,376] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:09:47,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgbadfc354-74d2-42f8-8752-97b10f354b1a/dqc_reference
[2023-06-13 00:09:49,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:09:49,327] [INFO] Task started: Prodigal
[2023-06-13 00:09:49,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg024c76cb-608a-4833-8459-70ae4eddc541/GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:09:53,539] [INFO] Task succeeded: Prodigal
[2023-06-13 00:09:53,539] [INFO] Task started: HMMsearch
[2023-06-13 00:09:53,540] [INFO] Running command: hmmsearch --tblout GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbadfc354-74d2-42f8-8752-97b10f354b1a/dqc_reference/reference_markers.hmm GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:09:53,777] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:09:53,779] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg024c76cb-608a-4833-8459-70ae4eddc541/GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-13 00:09:53,805] [INFO] Query marker FASTA was written to GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 00:09:53,806] [INFO] Task started: Blastn
[2023-06-13 00:09:53,806] [INFO] Running command: blastn -query GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbadfc354-74d2-42f8-8752-97b10f354b1a/dqc_reference/reference_markers.fasta -out GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:09:54,404] [INFO] Task succeeded: Blastn
[2023-06-13 00:09:54,412] [INFO] Selected 14 target genomes.
[2023-06-13 00:09:54,413] [INFO] Target genome list was writen to GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 00:09:54,483] [INFO] Task started: fastANI
[2023-06-13 00:09:54,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg024c76cb-608a-4833-8459-70ae4eddc541/GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:10:01,497] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:01,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbadfc354-74d2-42f8-8752-97b10f354b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:10:01,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbadfc354-74d2-42f8-8752-97b10f354b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:10:01,508] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 00:10:01,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 00:10:01,509] [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
Capnocytophaga leadbetteri	strain=DSM 22902	GCA_003054025.1	327575	327575	type	True	95.7029	226	250	95	conclusive
Capnocytophaga periodontitidis	strain=p1a2	GCA_016126015.1	2795027	2795027	type	True	80.8593	124	250	95	below_threshold
Capnocytophaga endodontalis	strain=ChDC OS43	GCA_002209445.1	2708117	2708117	type	True	80.6433	127	250	95	below_threshold
Capnocytophaga sputigena	strain=NCTC11653	GCA_900446695.1	1019	1019	type	True	79.8851	127	250	95	below_threshold
Capnocytophaga ochracea	strain=DSM 7271	GCA_000023285.1	1018	1018	type	True	79.3658	115	250	95	below_threshold
Capnocytophaga ochracea	strain=FDAARGOS_1468	GCA_019930725.1	1018	1018	type	True	79.3631	115	250	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:10:01,518] [INFO] DFAST Taxonomy check result was written to GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 00:10:01,519] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:10:01,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:10:01,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbadfc354-74d2-42f8-8752-97b10f354b1a/dqc_reference/checkm_data
[2023-06-13 00:10:01,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:10:01,550] [INFO] Task started: CheckM
[2023-06-13 00:10:01,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 00:10:20,735] [INFO] Task succeeded: CheckM
[2023-06-13 00:10:20,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:10:20,755] [INFO] ===== Completeness check finished =====
[2023-06-13 00:10:20,756] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:10:20,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 00:10:20,757] [INFO] Task started: Blastn
[2023-06-13 00:10:20,757] [INFO] Running command: blastn -query GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbadfc354-74d2-42f8-8752-97b10f354b1a/dqc_reference/reference_markers_gtdb.fasta -out GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:10:21,494] [INFO] Task succeeded: Blastn
[2023-06-13 00:10:21,501] [INFO] Selected 15 target genomes.
[2023-06-13 00:10:21,501] [INFO] Target genome list was writen to GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:10:21,513] [INFO] Task started: fastANI
[2023-06-13 00:10:21,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg024c76cb-608a-4833-8459-70ae4eddc541/GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:10:29,239] [INFO] Task succeeded: fastANI
[2023-06-13 00:10:29,249] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:10:29,249] [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_003054025.1	s__Capnocytophaga leadbetteri	95.7029	226	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	95.46	95.36	0.86	0.85	6	conclusive
GCF_017565765.1	s__Capnocytophaga bilenii	80.7	106	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.25	97.25	0.91	0.91	2	-
GCF_002209445.1	s__Capnocytophaga endodontalis	80.6433	127	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.66	96.51	0.90	0.87	9	-
GCF_002999135.1	s__Capnocytophaga sp002999135	80.4335	121	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900446695.1	s__Capnocytophaga sputigena	79.8424	128	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.52	96.32	0.92	0.88	8	-
GCF_000023285.1	s__Capnocytophaga ochracea	79.3658	115	250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.34	96.09	0.90	0.87	17	-
--------------------------------------------------------------------------------
[2023-06-13 00:10:29,251] [INFO] GTDB search result was written to GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 00:10:29,252] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:10:29,255] [INFO] DFAST_QC result json was written to GCA_947097735.1_SRR8786266_bin.7_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 00:10:29,255] [INFO] DFAST_QC completed!
[2023-06-13 00:10:29,255] [INFO] Total running time: 0h0m42s