[2023-06-30 09:37:05,110] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:37:05,113] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:37:05,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg62e566ab-67f8-48d4-b4ad-2513f958f241/dqc_reference
[2023-06-30 09:37:06,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:37:06,529] [INFO] Task started: Prodigal
[2023-06-30 09:37:06,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b6bde95-c6ef-4793-aa63-135fde6c6d09/GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:37:18,438] [INFO] Task succeeded: Prodigal
[2023-06-30 09:37:18,438] [INFO] Task started: HMMsearch
[2023-06-30 09:37:18,438] [INFO] Running command: hmmsearch --tblout GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62e566ab-67f8-48d4-b4ad-2513f958f241/dqc_reference/reference_markers.hmm GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:37:18,765] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:37:18,766] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0b6bde95-c6ef-4793-aa63-135fde6c6d09/GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-30 09:37:18,804] [INFO] Query marker FASTA was written to GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 09:37:18,805] [INFO] Task started: Blastn
[2023-06-30 09:37:18,805] [INFO] Running command: blastn -query GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg62e566ab-67f8-48d4-b4ad-2513f958f241/dqc_reference/reference_markers.fasta -out GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:37:19,459] [INFO] Task succeeded: Blastn
[2023-06-30 09:37:19,463] [INFO] Selected 25 target genomes.
[2023-06-30 09:37:19,463] [INFO] Target genome list was writen to GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 09:37:19,466] [INFO] Task started: fastANI
[2023-06-30 09:37:19,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b6bde95-c6ef-4793-aa63-135fde6c6d09/GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:37:37,806] [INFO] Task succeeded: fastANI
[2023-06-30 09:37:37,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62e566ab-67f8-48d4-b4ad-2513f958f241/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:37:37,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62e566ab-67f8-48d4-b4ad-2513f958f241/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:37:37,818] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:37:37,818] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 09:37:37,818] [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
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.6853	53	1524	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.6494	105	1524	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.4629	66	1524	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.4498	65	1524	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.4376	106	1524	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	76.2844	58	1524	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	76.2844	58	1524	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	76.2544	59	1524	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.1965	54	1524	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.0423	107	1524	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	75.8455	51	1524	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	75.4611	50	1524	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 09:37:37,820] [INFO] DFAST Taxonomy check result was written to GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 09:37:37,821] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:37:37,821] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:37:37,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62e566ab-67f8-48d4-b4ad-2513f958f241/dqc_reference/checkm_data
[2023-06-30 09:37:37,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:37:37,874] [INFO] Task started: CheckM
[2023-06-30 09:37:37,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 09:38:16,654] [INFO] Task succeeded: CheckM
[2023-06-30 09:38:16,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:38:16,680] [INFO] ===== Completeness check finished =====
[2023-06-30 09:38:16,680] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:38:16,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 09:38:16,681] [INFO] Task started: Blastn
[2023-06-30 09:38:16,681] [INFO] Running command: blastn -query GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg62e566ab-67f8-48d4-b4ad-2513f958f241/dqc_reference/reference_markers_gtdb.fasta -out GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:38:17,545] [INFO] Task succeeded: Blastn
[2023-06-30 09:38:17,550] [INFO] Selected 13 target genomes.
[2023-06-30 09:38:17,550] [INFO] Target genome list was writen to GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:38:17,553] [INFO] Task started: fastANI
[2023-06-30 09:38:17,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b6bde95-c6ef-4793-aa63-135fde6c6d09/GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:38:27,762] [INFO] Task succeeded: fastANI
[2023-06-30 09:38:27,773] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 09:38:27,773] [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_910578115.1	s__UBA3282 sp910578115	98.3042	1295	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009774655.1	s__UBA3282 sp009774655	88.5346	711	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.36	98.36	0.78	0.78	2	-
GCA_910588215.1	s__UBA3282 sp910588215	85.3771	901	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583895.1	s__Choladocola sp910583895	80.5081	79	1524	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_910578345.1	s__UBA3282 sp009774575	80.267	592	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.18	99.18	0.92	0.92	2	-
GCA_910575245.1	s__UBA3282 sp910575245	80.0666	647	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.49	99.49	0.95	0.95	2	-
GCA_910578555.1	s__UBA3282 sp910578555	78.5485	388	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804365.1	s__UBA3282 sp014804365	78.2634	304	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	96.35	96.35	0.82	0.82	2	-
GCA_003612405.1	s__UBA3282 sp003612405	78.0973	295	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.19	99.19	0.85	0.85	2	-
GCA_910579505.1	s__UBA3282 sp910579505	77.7566	233	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361355.1	s__UBA3282 sp002361355	77.5717	207	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.97	99.95	0.96	0.94	5	-
GCF_009695995.1	s__Acetatifactor intestinalis	76.2194	90	1524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.98	96.46	0.81	0.76	18	-
--------------------------------------------------------------------------------
[2023-06-30 09:38:27,775] [INFO] GTDB search result was written to GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 09:38:27,776] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:38:27,780] [INFO] DFAST_QC result json was written to GCA_946562415.1_SRR19792984_bin.6_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 09:38:27,780] [INFO] DFAST_QC completed!
[2023-06-30 09:38:27,781] [INFO] Total running time: 0h1m23s