[2023-06-08 14:46:48,608] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:46:48,613] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:46:48,613] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2e870a4-8fbe-41e0-b99d-8a95033cee77/dqc_reference
[2023-06-08 14:46:50,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:46:50,135] [INFO] Task started: Prodigal
[2023-06-08 14:46:50,136] [INFO] Running command: gunzip -c /var/lib/cwl/stgb75ef372-a392-4865-ad6b-c3a4167ad154/GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:47:08,212] [INFO] Task succeeded: Prodigal
[2023-06-08 14:47:08,213] [INFO] Task started: HMMsearch
[2023-06-08 14:47:08,213] [INFO] Running command: hmmsearch --tblout GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2e870a4-8fbe-41e0-b99d-8a95033cee77/dqc_reference/reference_markers.hmm GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:47:08,463] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:47:08,464] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb75ef372-a392-4865-ad6b-c3a4167ad154/GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 14:47:08,501] [INFO] Query marker FASTA was written to GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 14:47:08,502] [INFO] Task started: Blastn
[2023-06-08 14:47:08,502] [INFO] Running command: blastn -query GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2e870a4-8fbe-41e0-b99d-8a95033cee77/dqc_reference/reference_markers.fasta -out GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:47:09,004] [INFO] Task succeeded: Blastn
[2023-06-08 14:47:09,008] [INFO] Selected 13 target genomes.
[2023-06-08 14:47:09,008] [INFO] Target genome list was writen to GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 14:47:09,009] [INFO] Task started: fastANI
[2023-06-08 14:47:09,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgb75ef372-a392-4865-ad6b-c3a4167ad154/GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:47:20,691] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:20,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2e870a4-8fbe-41e0-b99d-8a95033cee77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:47:20,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2e870a4-8fbe-41e0-b99d-8a95033cee77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:47:20,708] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 14:47:20,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 14:47:20,709] [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 muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	98.2419	875	1015	95	conclusive
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	92.2597	739	1015	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	92.2378	760	1015	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	92.1732	749	1015	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	92.0927	759	1015	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	92.007	742	1015	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.0541	426	1015	95	below_threshold
Bacteroides stercorirosoris	strain=DSM 26884	GCA_900142015.1	871324	871324	type	True	79.1682	407	1015	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.1235	401	1015	95	below_threshold
Bacteroides intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	79.0155	369	1015	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	78.8561	365	1015	95	below_threshold
Bacteroides oleiciplenus	strain=YIT 12058	GCA_000315485.1	626931	626931	type	True	78.7038	412	1015	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	78.6828	355	1015	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:47:20,711] [INFO] DFAST Taxonomy check result was written to GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 14:47:20,711] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:47:20,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:47:20,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2e870a4-8fbe-41e0-b99d-8a95033cee77/dqc_reference/checkm_data
[2023-06-08 14:47:20,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:47:20,745] [INFO] Task started: CheckM
[2023-06-08 14:47:20,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 14:48:13,464] [INFO] Task succeeded: CheckM
[2023-06-08 14:48:13,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:48:13,487] [INFO] ===== Completeness check finished =====
[2023-06-08 14:48:13,487] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:48:13,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 14:48:13,488] [INFO] Task started: Blastn
[2023-06-08 14:48:13,488] [INFO] Running command: blastn -query GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2e870a4-8fbe-41e0-b99d-8a95033cee77/dqc_reference/reference_markers_gtdb.fasta -out GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:48:13,985] [INFO] Task succeeded: Blastn
[2023-06-08 14:48:13,989] [INFO] Selected 13 target genomes.
[2023-06-08 14:48:13,989] [INFO] Target genome list was writen to GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:48:13,999] [INFO] Task started: fastANI
[2023-06-08 14:48:13,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgb75ef372-a392-4865-ad6b-c3a4167ad154/GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:48:25,239] [INFO] Task succeeded: fastANI
[2023-06-08 14:48:25,262] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:48:25,262] [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_004793475.1	s__Bacteroides sp002491635	98.8801	922	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	conclusive
GCF_000154205.1	s__Bacteroides uniformis	92.1314	752	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_000614125.1	s__Bacteroides rodentium	91.0148	721	1015	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	86.6462	513	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	81.4114	537	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCA_902388495.1	s__Bacteroides sp902388495	81.1916	515	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000186225.1	s__Bacteroides helcogenes	79.4641	440	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342845.1	s__Bacteroides heparinolyticus	79.2898	417	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCF_900142015.1	s__Bacteroides stercorirosoris	79.168	408	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.49	98.12	0.84	0.77	7	-
GCF_000513195.1	s__Bacteroides timonensis	78.8561	365	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019129285.1	s__Bacteroides sp900552405	78.7764	380	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.09	95.34	0.92	0.76	12	-
GCF_003464595.1	s__Bacteroides intestinalis_A	78.7299	371	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	97.86	96.66	0.85	0.74	7	-
GCF_000158035.1	s__Bacteroides cellulosilyticus	78.6948	354	1015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.21	95.02	0.83	0.72	42	-
--------------------------------------------------------------------------------
[2023-06-08 14:48:25,264] [INFO] GTDB search result was written to GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 14:48:25,265] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:48:25,268] [INFO] DFAST_QC result json was written to GCA_947040525.1_ERR8099095_bin.16_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 14:48:25,269] [INFO] DFAST_QC completed!
[2023-06-08 14:48:25,269] [INFO] Total running time: 0h1m37s