[2023-06-18 20:56:22,763] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:22,792] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:22,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg936e072e-e86f-4316-a217-f75eb13d7998/dqc_reference
[2023-06-18 20:56:24,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:24,176] [INFO] Task started: Prodigal
[2023-06-18 20:56:24,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg626155c7-b444-4c08-802a-265a8b4dd0ac/GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:27,082] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:27,082] [INFO] Task started: HMMsearch
[2023-06-18 20:56:27,083] [INFO] Running command: hmmsearch --tblout GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg936e072e-e86f-4316-a217-f75eb13d7998/dqc_reference/reference_markers.hmm GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:27,336] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:27,338] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg626155c7-b444-4c08-802a-265a8b4dd0ac/GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-18 20:56:27,360] [INFO] Query marker FASTA was written to GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 20:56:27,361] [INFO] Task started: Blastn
[2023-06-18 20:56:27,361] [INFO] Running command: blastn -query GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg936e072e-e86f-4316-a217-f75eb13d7998/dqc_reference/reference_markers.fasta -out GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:28,239] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:28,244] [INFO] Selected 20 target genomes.
[2023-06-18 20:56:28,244] [INFO] Target genome list was writen to GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 20:56:28,250] [INFO] Task started: fastANI
[2023-06-18 20:56:28,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg626155c7-b444-4c08-802a-265a8b4dd0ac/GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:56:38,713] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:38,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg936e072e-e86f-4316-a217-f75eb13d7998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:56:38,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg936e072e-e86f-4316-a217-f75eb13d7998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:56:38,727] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:56:38,727] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:56:38,728] [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
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	75.128	53	540	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	75.1157	54	540	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	75.0674	61	540	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	75.0674	61	540	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	75.0664	55	540	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	75.0445	64	540	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	75.0432	61	540	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	75.0125	73	540	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	75.0068	57	540	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	74.9929	68	540	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	74.9193	51	540	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	74.9187	71	540	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	74.7673	59	540	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:56:38,731] [INFO] DFAST Taxonomy check result was written to GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 20:56:38,731] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:56:38,731] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:56:38,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg936e072e-e86f-4316-a217-f75eb13d7998/dqc_reference/checkm_data
[2023-06-18 20:56:38,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:56:38,767] [INFO] Task started: CheckM
[2023-06-18 20:56:38,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 20:56:55,580] [INFO] Task succeeded: CheckM
[2023-06-18 20:56:55,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:56:55,601] [INFO] ===== Completeness check finished =====
[2023-06-18 20:56:55,601] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:56:55,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 20:56:55,602] [INFO] Task started: Blastn
[2023-06-18 20:56:55,602] [INFO] Running command: blastn -query GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg936e072e-e86f-4316-a217-f75eb13d7998/dqc_reference/reference_markers_gtdb.fasta -out GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:56,352] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:56,355] [INFO] Selected 9 target genomes.
[2023-06-18 20:56:56,356] [INFO] Target genome list was writen to GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:56:56,388] [INFO] Task started: fastANI
[2023-06-18 20:56:56,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg626155c7-b444-4c08-802a-265a8b4dd0ac/GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:56:59,287] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:59,301] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:56:59,302] [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_905213875.1	s__CAG-269 sp905213875	98.4309	368	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.16	98.07	0.72	0.64	3	conclusive
GCA_014846485.1	s__CAG-269 sp014846485	90.3162	318	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762425.1	s__CAG-269 sp900762425	83.097	330	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554365.1	s__CAG-269 sp900554365	82.7356	278	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000431335.1	s__CAG-269 sp000431335	80.539	267	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.17	98.64	0.90	0.86	6	-
GCA_900556695.1	s__CAG-269 sp900556695	80.5314	166	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215845.1	s__CAG-269 sp905215845	80.3541	138	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553985.1	s__CAG-269 sp900553985	80.1137	231	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.48	98.04	0.82	0.80	5	-
GCA_001916055.1	s__CAG-269 sp001916055	79.19	180	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.37	97.96	0.88	0.86	4	-
--------------------------------------------------------------------------------
[2023-06-18 20:56:59,304] [INFO] GTDB search result was written to GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 20:56:59,304] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:56:59,308] [INFO] DFAST_QC result json was written to GCA_937950155.1_ERR479302_bin.27_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 20:56:59,308] [INFO] DFAST_QC completed!
[2023-06-18 20:56:59,308] [INFO] Total running time: 0h0m37s