[2023-06-07 21:13:30,482] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:13:30,485] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:13:30,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg557860ab-dedc-41d7-9f02-b05563400a17/dqc_reference
[2023-06-07 21:13:33,295] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:13:33,296] [INFO] Task started: Prodigal
[2023-06-07 21:13:33,296] [INFO] Running command: gunzip -c /var/lib/cwl/stg7263b48a-c92f-4e0f-b611-8d113acda7ab/GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:13:44,309] [INFO] Task succeeded: Prodigal
[2023-06-07 21:13:44,310] [INFO] Task started: HMMsearch
[2023-06-07 21:13:44,310] [INFO] Running command: hmmsearch --tblout GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg557860ab-dedc-41d7-9f02-b05563400a17/dqc_reference/reference_markers.hmm GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:13:44,602] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:13:44,604] [INFO] Found 6/6 markers.
[2023-06-07 21:13:44,645] [INFO] Query marker FASTA was written to GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 21:13:44,645] [INFO] Task started: Blastn
[2023-06-07 21:13:44,645] [INFO] Running command: blastn -query GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg557860ab-dedc-41d7-9f02-b05563400a17/dqc_reference/reference_markers.fasta -out GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:13:45,251] [INFO] Task succeeded: Blastn
[2023-06-07 21:13:45,255] [INFO] Selected 33 target genomes.
[2023-06-07 21:13:45,256] [INFO] Target genome list was writen to GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 21:13:45,257] [INFO] Task started: fastANI
[2023-06-07 21:13:45,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg7263b48a-c92f-4e0f-b611-8d113acda7ab/GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:14:03,089] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:03,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg557860ab-dedc-41d7-9f02-b05563400a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:14:03,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg557860ab-dedc-41d7-9f02-b05563400a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:14:03,101] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:14:03,101] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:14:03,101] [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
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	76.3502	71	1434	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.1029	56	1434	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	76.0817	54	1434	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	76.0713	56	1434	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.0572	58	1434	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.027	54	1434	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	76.0196	52	1434	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	75.9456	59	1434	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	75.8875	52	1434	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	75.8768	51	1434	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	75.7593	75	1434	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	75.6754	67	1434	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:14:03,104] [INFO] DFAST Taxonomy check result was written to GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 21:14:03,105] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:14:03,105] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:14:03,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg557860ab-dedc-41d7-9f02-b05563400a17/dqc_reference/checkm_data
[2023-06-07 21:14:03,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:14:03,150] [INFO] Task started: CheckM
[2023-06-07 21:14:03,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 21:14:39,679] [INFO] Task succeeded: CheckM
[2023-06-07 21:14:39,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:14:39,703] [INFO] ===== Completeness check finished =====
[2023-06-07 21:14:39,704] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:14:39,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 21:14:39,704] [INFO] Task started: Blastn
[2023-06-07 21:14:39,704] [INFO] Running command: blastn -query GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg557860ab-dedc-41d7-9f02-b05563400a17/dqc_reference/reference_markers_gtdb.fasta -out GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:14:40,491] [INFO] Task succeeded: Blastn
[2023-06-07 21:14:40,496] [INFO] Selected 16 target genomes.
[2023-06-07 21:14:40,496] [INFO] Target genome list was writen to GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:14:40,500] [INFO] Task started: fastANI
[2023-06-07 21:14:40,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg7263b48a-c92f-4e0f-b611-8d113acda7ab/GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:14:51,764] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:51,787] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:14:51,789] [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
GCA_910583615.1	s__Choladocola sp910583615	99.1589	1231	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910584205.1	s__Choladocola sp910584205	87.782	772	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574805.1	s__Choladocola sp009774135	85.2418	777	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	99.38	99.01	0.92	0.88	3	-
GCA_009774145.1	s__Choladocola sp009774145	84.8588	856	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	98.49	98.49	0.80	0.80	2	-
GCA_910587765.1	s__Choladocola sp910587765	81.7271	587	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584945.1	s__Choladocola sp910584945	81.1663	538	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579225.1	s__Choladocola sp910579225	80.5897	516	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583895.1	s__Choladocola sp910583895	80.2595	500	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774155.1	s__Choladocola sp009774155	78.8889	261	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	98.91	98.91	0.77	0.77	2	-
GCA_910585465.1	s__Choladocola sp910585465	78.4397	317	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018376135.1	s__Choladocola sp018376135	78.2985	295	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587495.1	s__Choladocola sp910587495	78.2511	295	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585995.1	s__Choladocola sp910585995	78.0397	315	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003480725.1	s__Choladocola sp003480725	76.9349	189	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladocola	95.0	97.99	97.12	0.84	0.75	9	-
GCF_008121495.1	s__Ruminococcus_B gnavus	76.082	57	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCF_900120345.1	s__Lachnoclostridium_B phocaeense	75.8238	60	1434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.08	98.08	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-07 21:14:51,796] [INFO] GTDB search result was written to GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 21:14:51,796] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:14:51,803] [INFO] DFAST_QC result json was written to GCA_947384045.1_ERR6760060_bin.80_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 21:14:51,803] [INFO] DFAST_QC completed!
[2023-06-07 21:14:51,803] [INFO] Total running time: 0h1m21s