[2023-06-13 07:31:58,842] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:31:58,848] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:31:58,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e6b884a-3bba-4a4f-8179-2a0f78d24ca7/dqc_reference
[2023-06-13 07:32:00,158] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:32:00,159] [INFO] Task started: Prodigal
[2023-06-13 07:32:00,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg94e9cb30-6b8c-4222-84e3-2381317ebf32/GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:32:13,054] [INFO] Task succeeded: Prodigal
[2023-06-13 07:32:13,055] [INFO] Task started: HMMsearch
[2023-06-13 07:32:13,055] [INFO] Running command: hmmsearch --tblout GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e6b884a-3bba-4a4f-8179-2a0f78d24ca7/dqc_reference/reference_markers.hmm GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:32:13,320] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:32:13,321] [INFO] Found 6/6 markers.
[2023-06-13 07:32:13,352] [INFO] Query marker FASTA was written to GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 07:32:13,352] [INFO] Task started: Blastn
[2023-06-13 07:32:13,353] [INFO] Running command: blastn -query GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e6b884a-3bba-4a4f-8179-2a0f78d24ca7/dqc_reference/reference_markers.fasta -out GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:32:13,959] [INFO] Task succeeded: Blastn
[2023-06-13 07:32:13,964] [INFO] Selected 18 target genomes.
[2023-06-13 07:32:13,965] [INFO] Target genome list was writen to GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 07:32:13,967] [INFO] Task started: fastANI
[2023-06-13 07:32:13,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg94e9cb30-6b8c-4222-84e3-2381317ebf32/GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 07:32:23,999] [INFO] Task succeeded: fastANI
[2023-06-13 07:32:24,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e6b884a-3bba-4a4f-8179-2a0f78d24ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 07:32:24,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e6b884a-3bba-4a4f-8179-2a0f78d24ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 07:32:24,014] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 07:32:24,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 07:32:24,015] [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 histicola	strain=JCM 15637	GCA_000613925.1	470565	470565	type	True	97.7296	823	929	95	conclusive
Prevotella jejuni	strain=DSM 26989	GCA_900187995.1	1177574	1177574	type	True	80.729	381	929	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	80.5445	368	929	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	80.494	372	929	95	below_threshold
Prevotella nanceiensis	strain=DSM 19126	GCA_000379965.1	425941	425941	type	True	80.4687	57	929	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	80.3433	338	929	95	below_threshold
Prevotella nanceiensis	strain=JCM 15639	GCA_000613985.1	425941	425941	type	True	80.3283	56	929	95	below_threshold
Prevotella scopos	strain=DSM 22613	GCA_900129535.1	589437	589437	type	True	79.9556	368	929	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	79.9481	379	929	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	79.9457	380	929	95	below_threshold
Prevotella scopos	strain=JCM 17725	GCA_000614285.1	589437	589437	type	True	79.904	365	929	95	below_threshold
Prevotella veroralis	strain=JCM 6290	GCA_000613325.1	28137	28137	type	True	79.8997	321	929	95	below_threshold
Prevotella veroralis	strain=DSM 19559	GCA_000377625.1	28137	28137	type	True	79.8148	325	929	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	79.5784	330	929	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	78.8652	235	929	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	78.7784	226	929	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 07:32:24,017] [INFO] DFAST Taxonomy check result was written to GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 07:32:24,017] [INFO] ===== Taxonomy check completed =====
[2023-06-13 07:32:24,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:32:24,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e6b884a-3bba-4a4f-8179-2a0f78d24ca7/dqc_reference/checkm_data
[2023-06-13 07:32:24,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:32:24,060] [INFO] Task started: CheckM
[2023-06-13 07:32:24,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 07:33:05,759] [INFO] Task succeeded: CheckM
[2023-06-13 07:33:05,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 07:33:05,779] [INFO] ===== Completeness check finished =====
[2023-06-13 07:33:05,780] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:33:05,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 07:33:05,781] [INFO] Task started: Blastn
[2023-06-13 07:33:05,781] [INFO] Running command: blastn -query GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e6b884a-3bba-4a4f-8179-2a0f78d24ca7/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:33:06,587] [INFO] Task succeeded: Blastn
[2023-06-13 07:33:06,592] [INFO] Selected 15 target genomes.
[2023-06-13 07:33:06,592] [INFO] Target genome list was writen to GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:33:06,598] [INFO] Task started: fastANI
[2023-06-13 07:33:06,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg94e9cb30-6b8c-4222-84e3-2381317ebf32/GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:33:15,887] [INFO] Task succeeded: fastANI
[2023-06-13 07:33:15,911] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 07:33:15,912] [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_000613925.1	s__Prevotella histicola	97.7296	823	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.59	0.91	0.86	21	conclusive
GCF_900187995.1	s__Prevotella jejuni	80.7537	380	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.57	0.92	0.88	7	-
GCF_000144405.1	s__Prevotella melaninogenica	80.561	367	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_018127965.1	s__Prevotella melaninogenica_B	80.3753	363	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_000379965.1	s__Prevotella nanceiensis	80.3638	58	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.31	96.77	0.96	0.91	12	-
GCF_000257925.1	s__Prevotella sp000257925	80.3605	336	929	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	80.2633	361	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127785.1	s__Prevotella scopos	79.9604	379	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	-
GCF_018128065.1	s__Prevotella sp000467895	79.858	342	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_000377625.1	s__Prevotella veroralis	79.8207	324	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.76	96.65	0.91	0.86	4	-
GCF_003609775.1	s__Prevotella melaninogenica_A	79.7166	371	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000163055.2	s__Prevotella sp000163055	78.9437	54	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454835.1	s__Prevotella denticola	78.8652	235	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	97.69	0.92	0.88	14	-
GCA_905236755.1	s__Prevotella sp905236755	77.5995	85	929	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	97.34	0.84	0.68	4	-
--------------------------------------------------------------------------------
[2023-06-13 07:33:15,914] [INFO] GTDB search result was written to GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 07:33:15,914] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:33:15,918] [INFO] DFAST_QC result json was written to GCA_938014195.1_SRR8114048_bin.2_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 07:33:15,918] [INFO] DFAST_QC completed!
[2023-06-13 07:33:15,918] [INFO] Total running time: 0h1m17s