[2023-06-08 11:22:25,920] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:22:25,923] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:22:25,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe7eac52-b3d2-4931-ba3a-fed85086429d/dqc_reference
[2023-06-08 11:22:27,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:22:27,179] [INFO] Task started: Prodigal
[2023-06-08 11:22:27,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a61d681-0e2b-4e74-be74-57fd6063a406/GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:22:46,116] [INFO] Task succeeded: Prodigal
[2023-06-08 11:22:46,117] [INFO] Task started: HMMsearch
[2023-06-08 11:22:46,117] [INFO] Running command: hmmsearch --tblout GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe7eac52-b3d2-4931-ba3a-fed85086429d/dqc_reference/reference_markers.hmm GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:22:46,382] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:22:46,384] [INFO] Found 6/6 markers.
[2023-06-08 11:22:46,418] [INFO] Query marker FASTA was written to GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:22:46,418] [INFO] Task started: Blastn
[2023-06-08 11:22:46,418] [INFO] Running command: blastn -query GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe7eac52-b3d2-4931-ba3a-fed85086429d/dqc_reference/reference_markers.fasta -out GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:22:47,026] [INFO] Task succeeded: Blastn
[2023-06-08 11:22:47,031] [INFO] Selected 27 target genomes.
[2023-06-08 11:22:47,031] [INFO] Target genome list was writen to GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:22:47,034] [INFO] Task started: fastANI
[2023-06-08 11:22:47,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a61d681-0e2b-4e74-be74-57fd6063a406/GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:23:04,329] [INFO] Task succeeded: fastANI
[2023-06-08 11:23:04,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe7eac52-b3d2-4931-ba3a-fed85086429d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:23:04,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe7eac52-b3d2-4931-ba3a-fed85086429d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:23:04,351] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 11:23:04,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 11:23:04,351] [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 fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	99.2873	955	1070	95	conclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	81.301	540	1070	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	81.2932	534	1070	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	81.2546	536	1070	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	81.2499	531	1070	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	81.2219	537	1070	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	81.0153	520	1070	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	80.8419	512	1070	95	below_threshold
Bacteroides helcogenes	strain=P 36-108	GCA_000186225.1	290053	290053	type	True	80.3624	508	1070	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	79.5862	435	1070	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	79.577	442	1070	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	79.5659	428	1070	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	79.547	442	1070	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.5442	440	1070	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	79.446	391	1070	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	79.4424	392	1070	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	79.3325	406	1070	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	79.3062	414	1070	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	79.3001	410	1070	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.7785	218	1070	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	77.6291	197	1070	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	77.5727	200	1070	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:23:04,353] [INFO] DFAST Taxonomy check result was written to GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:23:04,354] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:23:04,354] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:23:04,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe7eac52-b3d2-4931-ba3a-fed85086429d/dqc_reference/checkm_data
[2023-06-08 11:23:04,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:23:04,396] [INFO] Task started: CheckM
[2023-06-08 11:23:04,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:23:59,028] [INFO] Task succeeded: CheckM
[2023-06-08 11:23:59,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:23:59,052] [INFO] ===== Completeness check finished =====
[2023-06-08 11:23:59,052] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:23:59,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:23:59,053] [INFO] Task started: Blastn
[2023-06-08 11:23:59,053] [INFO] Running command: blastn -query GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe7eac52-b3d2-4931-ba3a-fed85086429d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:23:59,873] [INFO] Task succeeded: Blastn
[2023-06-08 11:23:59,878] [INFO] Selected 23 target genomes.
[2023-06-08 11:23:59,878] [INFO] Target genome list was writen to GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:23:59,906] [INFO] Task started: fastANI
[2023-06-08 11:23:59,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a61d681-0e2b-4e74-be74-57fd6063a406/GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:24:15,291] [INFO] Task succeeded: fastANI
[2023-06-08 11:24:15,310] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:24:15,310] [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_000195635.1	s__Bacteroides fluxus	99.2873	955	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	conclusive
GCF_000154205.1	s__Bacteroides uniformis	81.2218	537	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_004793475.1	s__Bacteroides sp002491635	81.1226	521	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCF_000614125.1	s__Bacteroides rodentium	81.0028	521	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197435.1	s__Bacteroides sp905197435	80.6211	376	1070	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	80.3624	508	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902388495.1	s__Bacteroides sp902388495	80.144	482	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCA_905203765.1	s__Bacteroides sp905203765	79.8634	338	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555635.1	s__Bacteroides sp900555635	79.6354	460	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.02	98.02	0.75	0.75	2	-
GCF_003438615.1	s__Bacteroides sp003545565	79.6268	414	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_900129655.1	s__Bacteroides clarus	79.5933	440	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000154525.1	s__Bacteroides stercoris	79.547	442	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_000374365.1	s__Bacteroides gallinarum	79.4387	393	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000155815.1	s__Bacteroides eggerthii	79.3112	414	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCA_910578895.1	s__Bacteroides sp910578895	79.2854	359	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900241005.1	s__Bacteroides cutis	79.0963	410	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.53	99.47	0.92	0.89	5	-
GCF_004342845.1	s__Bacteroides heparinolyticus	78.5491	339	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCA_905207245.1	s__Bacteroides sp905207245	78.4611	377	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108345.1	s__Bacteroides ndongoniae	77.9655	255	1070	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-08 11:24:15,312] [INFO] GTDB search result was written to GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:24:15,313] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:24:15,317] [INFO] DFAST_QC result json was written to GCA_945981045.1_SRR12203258_bin.5_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:24:15,317] [INFO] DFAST_QC completed!
[2023-06-08 11:24:15,318] [INFO] Total running time: 0h1m49s