[2023-06-16 23:43:37,990] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:43:37,994] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:43:37,994] [INFO] DQC Reference Directory: /var/lib/cwl/stg7468cdd4-bc30-4363-9dd2-51a269e541d1/dqc_reference
[2023-06-16 23:43:39,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:43:39,369] [INFO] Task started: Prodigal
[2023-06-16 23:43:39,369] [INFO] Running command: gunzip -c /var/lib/cwl/stgb64f3262-8763-4fd2-99d7-a8a3bd559e8f/GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna.gz | prodigal -d GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/cds.fna -a GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:44:00,931] [INFO] Task succeeded: Prodigal
[2023-06-16 23:44:00,932] [INFO] Task started: HMMsearch
[2023-06-16 23:44:00,932] [INFO] Running command: hmmsearch --tblout GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7468cdd4-bc30-4363-9dd2-51a269e541d1/dqc_reference/reference_markers.hmm GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:44:01,230] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:44:01,232] [INFO] Found 6/6 markers.
[2023-06-16 23:44:01,268] [INFO] Query marker FASTA was written to GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/markers.fasta
[2023-06-16 23:44:01,268] [INFO] Task started: Blastn
[2023-06-16 23:44:01,269] [INFO] Running command: blastn -query GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/markers.fasta -db /var/lib/cwl/stg7468cdd4-bc30-4363-9dd2-51a269e541d1/dqc_reference/reference_markers.fasta -out GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:44:01,943] [INFO] Task succeeded: Blastn
[2023-06-16 23:44:01,947] [INFO] Selected 21 target genomes.
[2023-06-16 23:44:01,948] [INFO] Target genome list was writen to GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/target_genomes.txt
[2023-06-16 23:44:01,975] [INFO] Task started: fastANI
[2023-06-16 23:44:01,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgb64f3262-8763-4fd2-99d7-a8a3bd559e8f/GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna.gz --refList GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/target_genomes.txt --output GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:44:17,933] [INFO] Task succeeded: fastANI
[2023-06-16 23:44:17,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7468cdd4-bc30-4363-9dd2-51a269e541d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:44:17,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7468cdd4-bc30-4363-9dd2-51a269e541d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:44:17,958] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:44:17,958] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 23:44:17,958] [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
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	82.5267	385	1265	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	82.4153	384	1265	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	80.8678	335	1265	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.2772	308	1265	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	79.2753	300	1265	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	79.2396	304	1265	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.2228	345	1265	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	78.9935	361	1265	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	78.818	334	1265	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.8139	301	1265	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	78.7742	345	1265	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.7709	298	1265	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	78.7542	345	1265	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	78.7466	340	1265	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	78.7243	297	1265	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	78.7236	304	1265	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	78.5674	289	1265	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	78.5411	288	1265	95	below_threshold
Bacteroides fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	78.3292	302	1265	95	below_threshold
Bacteroides helcogenes	strain=P 36-108	GCA_000186225.1	290053	290053	type	True	78.1254	252	1265	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.9621	207	1265	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 23:44:17,962] [INFO] DFAST Taxonomy check result was written to GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/tc_result.tsv
[2023-06-16 23:44:17,963] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:44:17,963] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:44:17,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7468cdd4-bc30-4363-9dd2-51a269e541d1/dqc_reference/checkm_data
[2023-06-16 23:44:17,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:44:18,015] [INFO] Task started: CheckM
[2023-06-16 23:44:18,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/checkm_input GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/checkm_result
[2023-06-16 23:45:17,733] [INFO] Task succeeded: CheckM
[2023-06-16 23:45:17,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 23:45:17,758] [INFO] ===== Completeness check finished =====
[2023-06-16 23:45:17,758] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:45:17,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/markers.fasta)
[2023-06-16 23:45:17,759] [INFO] Task started: Blastn
[2023-06-16 23:45:17,759] [INFO] Running command: blastn -query GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/markers.fasta -db /var/lib/cwl/stg7468cdd4-bc30-4363-9dd2-51a269e541d1/dqc_reference/reference_markers_gtdb.fasta -out GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:45:18,607] [INFO] Task succeeded: Blastn
[2023-06-16 23:45:18,613] [INFO] Selected 18 target genomes.
[2023-06-16 23:45:18,613] [INFO] Target genome list was writen to GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:45:18,624] [INFO] Task started: fastANI
[2023-06-16 23:45:18,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgb64f3262-8763-4fd2-99d7-a8a3bd559e8f/GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna.gz --refList GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/target_genomes_gtdb.txt --output GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:45:31,904] [INFO] Task succeeded: fastANI
[2023-06-16 23:45:31,922] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 23:45:31,922] [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_900108345.1	s__Bacteroides ndongoniae	97.8172	1045	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	conclusive
GCA_905201685.1	s__Bacteroides sp905201685	88.2117	405	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	82.4361	383	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900130135.1	s__Bacteroides togonis	81.9181	463	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCF_900128475.1	s__Bacteroides massiliensis	81.7434	502	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCA_019116805.1	s__Bacteroides merdavium	80.2378	362	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154525.1	s__Bacteroides stercoris	79.2492	305	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_000614125.1	s__Bacteroides rodentium	79.0318	358	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154205.1	s__Bacteroides uniformis	78.7796	344	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCA_902388495.1	s__Bacteroides sp902388495	78.6669	320	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCA_910578895.1	s__Bacteroides sp910578895	78.6521	290	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129655.1	s__Bacteroides clarus	78.5325	288	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000195635.1	s__Bacteroides fluxus	78.3666	299	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_003464595.1	s__Bacteroides intestinalis_A	78.2084	245	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	97.86	96.66	0.85	0.74	7	-
GCA_905203765.1	s__Bacteroides sp905203765	78.185	239	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186225.1	s__Bacteroides helcogenes	78.1254	252	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902364365.1	s__Bacteroides sp900556215	78.0675	245	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCA_017471925.1	s__Bacteroides sp017471925	77.9104	225	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 23:45:31,925] [INFO] GTDB search result was written to GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/result_gtdb.tsv
[2023-06-16 23:45:31,926] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:45:31,930] [INFO] DFAST_QC result json was written to GCA_905193705.1_ERR321530-mag-bin.9_genomic.fna/dqc_result.json
[2023-06-16 23:45:31,930] [INFO] DFAST_QC completed!
[2023-06-16 23:45:31,931] [INFO] Total running time: 0h1m54s