[2023-06-05 13:16:17,639] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:16:17,642] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:16:17,642] [INFO] DQC Reference Directory: /var/lib/cwl/stge0929062-6abd-4b83-b76e-635012f7efcb/dqc_reference
[2023-06-05 13:16:18,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:16:18,827] [INFO] Task started: Prodigal
[2023-06-05 13:16:18,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e14815f-6541-4730-b0ae-d5917db39bf3/GCA_934832875.1_MTG223_bin.8.fa_genomic.fna.gz | prodigal -d GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/cds.fna -a GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:16:23,597] [INFO] Task succeeded: Prodigal
[2023-06-05 13:16:23,598] [INFO] Task started: HMMsearch
[2023-06-05 13:16:23,598] [INFO] Running command: hmmsearch --tblout GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0929062-6abd-4b83-b76e-635012f7efcb/dqc_reference/reference_markers.hmm GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:16:23,822] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:16:23,824] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e14815f-6541-4730-b0ae-d5917db39bf3/GCA_934832875.1_MTG223_bin.8.fa_genomic.fna.gz]
[2023-06-05 13:16:23,854] [INFO] Query marker FASTA was written to GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/markers.fasta
[2023-06-05 13:16:23,855] [INFO] Task started: Blastn
[2023-06-05 13:16:23,855] [INFO] Running command: blastn -query GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stge0929062-6abd-4b83-b76e-635012f7efcb/dqc_reference/reference_markers.fasta -out GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:16:24,463] [INFO] Task succeeded: Blastn
[2023-06-05 13:16:24,469] [INFO] Selected 26 target genomes.
[2023-06-05 13:16:24,469] [INFO] Target genome list was writen to GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/target_genomes.txt
[2023-06-05 13:16:24,472] [INFO] Task started: fastANI
[2023-06-05 13:16:24,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e14815f-6541-4730-b0ae-d5917db39bf3/GCA_934832875.1_MTG223_bin.8.fa_genomic.fna.gz --refList GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/target_genomes.txt --output GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:16:41,078] [INFO] Task succeeded: fastANI
[2023-06-05 13:16:41,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0929062-6abd-4b83-b76e-635012f7efcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:16:41,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0929062-6abd-4b83-b76e-635012f7efcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:16:41,088] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:16:41,089] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:16:41,089] [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
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	76.9134	124	631	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.4567	62	631	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.4109	62	631	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.277	67	631	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.1155	67	631	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.0481	69	631	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:16:41,091] [INFO] DFAST Taxonomy check result was written to GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/tc_result.tsv
[2023-06-05 13:16:41,092] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:16:41,092] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:16:41,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0929062-6abd-4b83-b76e-635012f7efcb/dqc_reference/checkm_data
[2023-06-05 13:16:41,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:16:41,118] [INFO] Task started: CheckM
[2023-06-05 13:16:41,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/checkm_input GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/checkm_result
[2023-06-05 13:17:02,452] [INFO] Task succeeded: CheckM
[2023-06-05 13:17:02,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:17:02,477] [INFO] ===== Completeness check finished =====
[2023-06-05 13:17:02,477] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:17:02,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/markers.fasta)
[2023-06-05 13:17:02,479] [INFO] Task started: Blastn
[2023-06-05 13:17:02,480] [INFO] Running command: blastn -query GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stge0929062-6abd-4b83-b76e-635012f7efcb/dqc_reference/reference_markers_gtdb.fasta -out GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:17:03,418] [INFO] Task succeeded: Blastn
[2023-06-05 13:17:03,423] [INFO] Selected 12 target genomes.
[2023-06-05 13:17:03,423] [INFO] Target genome list was writen to GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:17:03,427] [INFO] Task started: fastANI
[2023-06-05 13:17:03,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e14815f-6541-4730-b0ae-d5917db39bf3/GCA_934832875.1_MTG223_bin.8.fa_genomic.fna.gz --refList GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:17:10,010] [INFO] Task succeeded: fastANI
[2023-06-05 13:17:10,022] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:17:10,022] [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_003435375.1	s__Copromonas sp900066535	98.0395	600	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.23	95.52	0.82	0.74	22	conclusive
GCF_003480435.1	s__Copromonas sp900066055	92.9435	543	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.09	96.90	0.88	0.80	7	-
GCF_003478035.1	s__Copromonas sp900066785	88.6017	539	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.14	96.17	0.83	0.76	16	-
GCA_900556965.1	s__Copromonas sp900556965	78.1468	85	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017482945.1	s__Copromonas sp017482945	77.9803	143	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435025.1	s__Copromonas sp017435025	77.7172	102	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385265.1	s__Copromonas sp000435795	77.5176	161	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	96.73	0.89	0.84	6	-
GCA_905215775.1	s__Copromonas sp905215775	77.3833	174	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223415.1	s__Copromonas sp900541255	77.3769	159	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	99.81	99.68	0.96	0.93	4	-
GCA_016302185.1	s__Clostridium_Q sp016302185	76.1395	58	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155545.1	s__Lacrimispora sp900155545	76.0889	64	631	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 13:17:10,024] [INFO] GTDB search result was written to GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 13:17:10,025] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:17:10,028] [INFO] DFAST_QC result json was written to GCA_934832875.1_MTG223_bin.8.fa_genomic.fna/dqc_result.json
[2023-06-05 13:17:10,028] [INFO] DFAST_QC completed!
[2023-06-05 13:17:10,028] [INFO] Total running time: 0h0m52s