[2023-07-01 01:49:53,839] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:49:53,842] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:49:53,842] [INFO] DQC Reference Directory: /var/lib/cwl/stgf43c1012-614b-408d-8a60-b5e315bb4d2b/dqc_reference
[2023-07-01 01:49:55,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:49:55,253] [INFO] Task started: Prodigal
[2023-07-01 01:49:55,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b4d5b29-6e37-426b-a332-8693f0b06b55/GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna.gz | prodigal -d GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/cds.fna -a GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:50:07,864] [INFO] Task succeeded: Prodigal
[2023-07-01 01:50:07,864] [INFO] Task started: HMMsearch
[2023-07-01 01:50:07,864] [INFO] Running command: hmmsearch --tblout GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf43c1012-614b-408d-8a60-b5e315bb4d2b/dqc_reference/reference_markers.hmm GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:50:08,135] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:50:08,136] [INFO] Found 6/6 markers.
[2023-07-01 01:50:08,166] [INFO] Query marker FASTA was written to GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/markers.fasta
[2023-07-01 01:50:08,167] [INFO] Task started: Blastn
[2023-07-01 01:50:08,167] [INFO] Running command: blastn -query GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf43c1012-614b-408d-8a60-b5e315bb4d2b/dqc_reference/reference_markers.fasta -out GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:50:08,817] [INFO] Task succeeded: Blastn
[2023-07-01 01:50:08,821] [INFO] Selected 21 target genomes.
[2023-07-01 01:50:08,822] [INFO] Target genome list was writen to GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/target_genomes.txt
[2023-07-01 01:50:08,827] [INFO] Task started: fastANI
[2023-07-01 01:50:08,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b4d5b29-6e37-426b-a332-8693f0b06b55/GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna.gz --refList GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/target_genomes.txt --output GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:50:20,563] [INFO] Task succeeded: fastANI
[2023-07-01 01:50:20,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf43c1012-614b-408d-8a60-b5e315bb4d2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:50:20,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf43c1012-614b-408d-8a60-b5e315bb4d2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:50:20,590] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-07-01 01:50:20,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-07-01 01:50:20,591] [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
Prevotella brunnea	strain=A2672	GCA_008016795.1	2508867	2508867	type	True	98.9372	602	705	95	conclusive
Prevotella corporis	strain=JCM 8529	GCA_000613365.1	28128	28128	type	True	84.0951	293	705	95	below_threshold
Prevotella corporis	strain=DSM 18810	GCA_000430525.1	28128	28128	type	True	84.0321	294	705	95	below_threshold
Prevotella ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	80.2111	115	705	95	below_threshold
Prevotella disiens	strain=NCTC11157	GCA_900454955.1	28130	28130	type	True	78.9263	134	705	95	below_threshold
Prevotella disiens	strain=ATCC 29426	GCA_000467875.1	28130	28130	type	True	78.6459	119	705	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	78.4508	69	705	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	78.2591	59	705	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	77.8639	81	705	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.8204	82	705	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	77.7336	85	705	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	77.6114	62	705	95	below_threshold
Prevotella pallens	strain=ATCC 700821	GCA_000220255.1	60133	60133	type	True	77.4398	82	705	95	below_threshold
Prevotella micans	strain=DSM 21469	GCA_000373705.1	189723	189723	type	True	77.3321	52	705	95	below_threshold
Prevotella pallens	strain=DSM 18710	GCA_003269195.1	60133	60133	type	True	77.3272	81	705	95	below_threshold
Prevotella micans	strain=JCM 16134	GCA_000614105.1	189723	189723	type	True	77.2815	52	705	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	77.0909	87	705	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	77.0435	101	705	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	76.6797	52	705	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:50:20,593] [INFO] DFAST Taxonomy check result was written to GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/tc_result.tsv
[2023-07-01 01:50:20,594] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:50:20,594] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:50:20,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf43c1012-614b-408d-8a60-b5e315bb4d2b/dqc_reference/checkm_data
[2023-07-01 01:50:20,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:50:20,637] [INFO] Task started: CheckM
[2023-07-01 01:50:20,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/checkm_input GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/checkm_result
[2023-07-01 01:51:01,279] [INFO] Task succeeded: CheckM
[2023-07-01 01:51:01,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:51:01,302] [INFO] ===== Completeness check finished =====
[2023-07-01 01:51:01,302] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:51:01,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/markers.fasta)
[2023-07-01 01:51:01,303] [INFO] Task started: Blastn
[2023-07-01 01:51:01,303] [INFO] Running command: blastn -query GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf43c1012-614b-408d-8a60-b5e315bb4d2b/dqc_reference/reference_markers_gtdb.fasta -out GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:51:02,054] [INFO] Task succeeded: Blastn
[2023-07-01 01:51:02,058] [INFO] Selected 23 target genomes.
[2023-07-01 01:51:02,058] [INFO] Target genome list was writen to GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:51:02,088] [INFO] Task started: fastANI
[2023-07-01 01:51:02,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b4d5b29-6e37-426b-a332-8693f0b06b55/GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna.gz --refList GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:51:13,747] [INFO] Task succeeded: fastANI
[2023-07-01 01:51:13,763] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:51:13,764] [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_008016795.1	s__Prevotella brunnea	98.9372	602	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.23	99.23	0.96	0.96	2	conclusive
GCF_000430525.1	s__Prevotella corporis	84.0933	294	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.63	97.78	0.92	0.87	4	-
GCF_900155655.1	s__Prevotella ihumii	80.2623	114	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262015.1	s__Prevotella fusca	77.8204	82	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000144405.1	s__Prevotella melaninogenica	77.6114	62	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_000257925.1	s__Prevotella sp000257925	77.5071	56	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
GCF_018127925.1	s__Prevotella melaninogenica_C	77.4635	67	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220255.1	s__Prevotella pallens	77.4398	82	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	96.89	0.94	0.88	40	-
GCF_000688375.1	s__Prevotella sp000688375	77.3881	148	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613945.1	s__Prevotella falsenii	77.3645	109	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614105.1	s__Prevotella micans	77.2815	52	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.39	98.24	0.98	0.95	4	-
GCF_000614025.1	s__Prevotella aurantiaca	77.0903	87	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_000614065.1	s__Prevotella dentasini	77.0435	101	705	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:51:13,765] [INFO] GTDB search result was written to GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/result_gtdb.tsv
[2023-07-01 01:51:13,766] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:51:13,769] [INFO] DFAST_QC result json was written to GCA_943912445.1_sxO41aIhQN_bin.63.MAG_genomic.fna/dqc_result.json
[2023-07-01 01:51:13,770] [INFO] DFAST_QC completed!
[2023-07-01 01:51:13,770] [INFO] Total running time: 0h1m20s