[2023-06-08 10:40:57,297] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:40:57,301] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:40:57,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg13e531f5-5316-4020-b6aa-f2e665a6496d/dqc_reference
[2023-06-08 10:40:58,716] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:40:58,717] [INFO] Task started: Prodigal
[2023-06-08 10:40:58,718] [INFO] Running command: gunzip -c /var/lib/cwl/stgd04c1fcf-204c-4666-aad5-c18a851be3a1/GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:41:18,406] [INFO] Task succeeded: Prodigal
[2023-06-08 10:41:18,407] [INFO] Task started: HMMsearch
[2023-06-08 10:41:18,407] [INFO] Running command: hmmsearch --tblout GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13e531f5-5316-4020-b6aa-f2e665a6496d/dqc_reference/reference_markers.hmm GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:41:18,699] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:41:18,700] [INFO] Found 6/6 markers.
[2023-06-08 10:41:18,731] [INFO] Query marker FASTA was written to GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 10:41:18,731] [INFO] Task started: Blastn
[2023-06-08 10:41:18,731] [INFO] Running command: blastn -query GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e531f5-5316-4020-b6aa-f2e665a6496d/dqc_reference/reference_markers.fasta -out GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:41:19,365] [INFO] Task succeeded: Blastn
[2023-06-08 10:41:19,370] [INFO] Selected 19 target genomes.
[2023-06-08 10:41:19,370] [INFO] Target genome list was writen to GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 10:41:19,398] [INFO] Task started: fastANI
[2023-06-08 10:41:19,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04c1fcf-204c-4666-aad5-c18a851be3a1/GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:41:33,025] [INFO] Task succeeded: fastANI
[2023-06-08 10:41:33,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13e531f5-5316-4020-b6aa-f2e665a6496d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:41:33,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13e531f5-5316-4020-b6aa-f2e665a6496d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:41:33,041] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:41:33,041] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 10:41:33,041] [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
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	78.0614	141	997	95	below_threshold
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	77.9834	137	997	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	77.5989	160	997	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	77.5989	160	997	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	77.5444	159	997	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	77.5069	168	997	95	below_threshold
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	77.2955	171	997	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	77.2883	160	997	95	below_threshold
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	77.2853	161	997	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	77.2816	160	997	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	76.8313	75	997	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	76.7818	77	997	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	76.7595	68	997	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 10:41:33,043] [INFO] DFAST Taxonomy check result was written to GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 10:41:33,044] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:41:33,044] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:41:33,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13e531f5-5316-4020-b6aa-f2e665a6496d/dqc_reference/checkm_data
[2023-06-08 10:41:33,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:41:33,083] [INFO] Task started: CheckM
[2023-06-08 10:41:33,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 10:42:29,118] [INFO] Task succeeded: CheckM
[2023-06-08 10:42:29,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:42:29,143] [INFO] ===== Completeness check finished =====
[2023-06-08 10:42:29,143] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:42:29,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 10:42:29,144] [INFO] Task started: Blastn
[2023-06-08 10:42:29,144] [INFO] Running command: blastn -query GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg13e531f5-5316-4020-b6aa-f2e665a6496d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:42:29,960] [INFO] Task succeeded: Blastn
[2023-06-08 10:42:29,965] [INFO] Selected 27 target genomes.
[2023-06-08 10:42:29,965] [INFO] Target genome list was writen to GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:42:29,973] [INFO] Task started: fastANI
[2023-06-08 10:42:29,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04c1fcf-204c-4666-aad5-c18a851be3a1/GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:42:44,109] [INFO] Task succeeded: fastANI
[2023-06-08 10:42:44,127] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:42:44,127] [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_004562445.1	s__Parabacteroides sp004562445	97.7143	523	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900770835.1	s__Parabacteroides sp900770835	78.1177	182	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012845.1	s__Parabacteroides distasonis	78.0324	133	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.16	96.57	0.86	0.75	191	-
GCF_004793765.1	s__Parabacteroides distasonis_A	77.9694	133	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.06	98.88	0.88	0.86	4	-
GCA_000436495.1	s__Parabacteroides faecavium	77.8816	113	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	96.87	96.42	0.81	0.77	5	-
GCF_014287585.1	s__Parabacteroides sp014287585	77.6618	177	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCA_017560165.1	s__Parabacteroides sp017560165	77.6444	54	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363715.1	s__Parabacteroides acidifaciens	77.5984	160	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCA_910577325.1	s__Parabacteroides sp910577325	77.5611	138	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038785.1	s__Parabacteroides sp011038785	77.55	126	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937385.1	s__Parabacteroides sp017937385	77.4808	167	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156495.1	s__Parabacteroides johnsonii	77.4184	163	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCF_000154105.1	s__Parabacteroides merdae	77.3199	158	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCF_014647375.1	s__Parabacteroides faecis	77.3097	170	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.52	97.91	0.91	0.84	9	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	77.0929	115	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013618865.1	s__Phocaeicola sp900541515	76.7318	67	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCA_004558305.1	s__Phocaeicola plebeius_B	76.2226	70	997	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 10:42:44,133] [INFO] GTDB search result was written to GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 10:42:44,133] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:42:44,138] [INFO] DFAST_QC result json was written to GCA_945987645.1_ERR2020026_bin.8_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 10:42:44,138] [INFO] DFAST_QC completed!
[2023-06-08 10:42:44,138] [INFO] Total running time: 0h1m47s