[2023-06-08 10:41:07,088] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:41:07,090] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:41:07,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ca132b8-9422-4528-be02-a8efccf2e281/dqc_reference
[2023-06-08 10:41:08,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:41:08,957] [INFO] Task started: Prodigal
[2023-06-08 10:41:08,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f24af38-ab7b-4f53-a26d-74ffc60f75c8/GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:41:17,160] [INFO] Task succeeded: Prodigal
[2023-06-08 10:41:17,161] [INFO] Task started: HMMsearch
[2023-06-08 10:41:17,161] [INFO] Running command: hmmsearch --tblout GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ca132b8-9422-4528-be02-a8efccf2e281/dqc_reference/reference_markers.hmm GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:41:17,396] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:41:17,398] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8f24af38-ab7b-4f53-a26d-74ffc60f75c8/GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 10:41:17,432] [INFO] Query marker FASTA was written to GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 10:41:17,433] [INFO] Task started: Blastn
[2023-06-08 10:41:17,433] [INFO] Running command: blastn -query GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ca132b8-9422-4528-be02-a8efccf2e281/dqc_reference/reference_markers.fasta -out GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:41:17,904] [INFO] Task succeeded: Blastn
[2023-06-08 10:41:17,917] [INFO] Selected 17 target genomes.
[2023-06-08 10:41:17,918] [INFO] Target genome list was writen to GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 10:41:17,920] [INFO] Task started: fastANI
[2023-06-08 10:41:17,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f24af38-ab7b-4f53-a26d-74ffc60f75c8/GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:41:27,409] [INFO] Task succeeded: fastANI
[2023-06-08 10:41:27,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ca132b8-9422-4528-be02-a8efccf2e281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:41:27,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ca132b8-9422-4528-be02-a8efccf2e281/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:41:27,416] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:41:27,416] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 10:41:27,416] [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
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	77.7401	51	1061	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 10:41:27,418] [INFO] DFAST Taxonomy check result was written to GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 10:41:27,419] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:41:27,419] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:41:27,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ca132b8-9422-4528-be02-a8efccf2e281/dqc_reference/checkm_data
[2023-06-08 10:41:27,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:41:27,461] [INFO] Task started: CheckM
[2023-06-08 10:41:27,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 10:41:57,235] [INFO] Task succeeded: CheckM
[2023-06-08 10:41:57,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:41:57,254] [INFO] ===== Completeness check finished =====
[2023-06-08 10:41:57,254] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:41:57,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 10:41:57,255] [INFO] Task started: Blastn
[2023-06-08 10:41:57,255] [INFO] Running command: blastn -query GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ca132b8-9422-4528-be02-a8efccf2e281/dqc_reference/reference_markers_gtdb.fasta -out GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:41:57,683] [INFO] Task succeeded: Blastn
[2023-06-08 10:41:57,688] [INFO] Selected 14 target genomes.
[2023-06-08 10:41:57,688] [INFO] Target genome list was writen to GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:41:57,691] [INFO] Task started: fastANI
[2023-06-08 10:41:57,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f24af38-ab7b-4f53-a26d-74ffc60f75c8/GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:42:06,700] [INFO] Task succeeded: fastANI
[2023-06-08 10:42:06,713] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:42:06,713] [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_910587295.1	s__CAG-95 sp910587295	99.0857	967	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014804285.1	s__CAG-95 sp014804285	78.2386	215	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911035.1	s__CAG-95 sp009911035	78.1967	234	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	96.92	95.99	0.83	0.79	4	-
GCA_000403495.2	s__CAG-95 sp000403495	78.1156	165	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.68	98.68	0.87	0.87	2	-
GCA_002492465.1	s__CAG-95 sp002492465	77.3189	179	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774465.1	s__CAG-95 sp009774465	77.0087	176	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.09	98.09	0.83	0.83	2	-
GCA_900553305.1	s__CAG-95 sp900553305	76.774	85	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
GCA_910579505.1	s__UBA3282 sp910579505	76.6964	78	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588215.1	s__UBA3282 sp910588215	76.6813	112	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438155.1	s__CAG-95 sp000438155	76.6451	94	1061	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.06	97.32	0.83	0.81	5	-
--------------------------------------------------------------------------------
[2023-06-08 10:42:06,715] [INFO] GTDB search result was written to GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 10:42:06,716] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:42:06,718] [INFO] DFAST_QC result json was written to GCA_949123035.1_ERR4467355_bin.3_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 10:42:06,719] [INFO] DFAST_QC completed!
[2023-06-08 10:42:06,719] [INFO] Total running time: 0h0m60s