[2023-06-05 05:03:24,949] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:03:24,951] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:03:24,951] [INFO] DQC Reference Directory: /var/lib/cwl/stgb52d320e-2373-4b1d-aa98-0fdd2852e45c/dqc_reference
[2023-06-05 05:03:26,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:03:26,327] [INFO] Task started: Prodigal
[2023-06-05 05:03:26,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg2583a0d9-5838-47f7-a33f-fe7bb3d6741d/GCA_934320635.1_ERR7738535_bin.86_genomic.fna.gz | prodigal -d GCA_934320635.1_ERR7738535_bin.86_genomic.fna/cds.fna -a GCA_934320635.1_ERR7738535_bin.86_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:03:31,139] [INFO] Task succeeded: Prodigal
[2023-06-05 05:03:31,139] [INFO] Task started: HMMsearch
[2023-06-05 05:03:31,139] [INFO] Running command: hmmsearch --tblout GCA_934320635.1_ERR7738535_bin.86_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb52d320e-2373-4b1d-aa98-0fdd2852e45c/dqc_reference/reference_markers.hmm GCA_934320635.1_ERR7738535_bin.86_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:03:31,436] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:03:31,437] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2583a0d9-5838-47f7-a33f-fe7bb3d6741d/GCA_934320635.1_ERR7738535_bin.86_genomic.fna.gz]
[2023-06-05 05:03:31,465] [INFO] Query marker FASTA was written to GCA_934320635.1_ERR7738535_bin.86_genomic.fna/markers.fasta
[2023-06-05 05:03:31,465] [INFO] Task started: Blastn
[2023-06-05 05:03:31,466] [INFO] Running command: blastn -query GCA_934320635.1_ERR7738535_bin.86_genomic.fna/markers.fasta -db /var/lib/cwl/stgb52d320e-2373-4b1d-aa98-0fdd2852e45c/dqc_reference/reference_markers.fasta -out GCA_934320635.1_ERR7738535_bin.86_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:03:32,166] [INFO] Task succeeded: Blastn
[2023-06-05 05:03:32,189] [INFO] Selected 16 target genomes.
[2023-06-05 05:03:32,190] [INFO] Target genome list was writen to GCA_934320635.1_ERR7738535_bin.86_genomic.fna/target_genomes.txt
[2023-06-05 05:03:32,193] [INFO] Task started: fastANI
[2023-06-05 05:03:32,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg2583a0d9-5838-47f7-a33f-fe7bb3d6741d/GCA_934320635.1_ERR7738535_bin.86_genomic.fna.gz --refList GCA_934320635.1_ERR7738535_bin.86_genomic.fna/target_genomes.txt --output GCA_934320635.1_ERR7738535_bin.86_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:03:40,077] [INFO] Task succeeded: fastANI
[2023-06-05 05:03:40,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb52d320e-2373-4b1d-aa98-0fdd2852e45c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:03:40,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb52d320e-2373-4b1d-aa98-0fdd2852e45c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:03:40,089] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 05:03:40,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 05:03:40,090] [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
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	99.6276	641	671	95	conclusive
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	78.7256	167	671	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.5958	141	671	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.4574	148	671	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.3774	160	671	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.1881	160	671	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.9919	161	671	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.9709	158	671	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.6472	62	671	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.299	81	671	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.1408	81	671	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.9487	57	671	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 05:03:40,092] [INFO] DFAST Taxonomy check result was written to GCA_934320635.1_ERR7738535_bin.86_genomic.fna/tc_result.tsv
[2023-06-05 05:03:40,092] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:03:40,092] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:03:40,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb52d320e-2373-4b1d-aa98-0fdd2852e45c/dqc_reference/checkm_data
[2023-06-05 05:03:40,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:03:40,119] [INFO] Task started: CheckM
[2023-06-05 05:03:40,119] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934320635.1_ERR7738535_bin.86_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934320635.1_ERR7738535_bin.86_genomic.fna/checkm_input GCA_934320635.1_ERR7738535_bin.86_genomic.fna/checkm_result
[2023-06-05 05:04:02,288] [INFO] Task succeeded: CheckM
[2023-06-05 05:04:02,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:04:02,303] [INFO] ===== Completeness check finished =====
[2023-06-05 05:04:02,303] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:04:02,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934320635.1_ERR7738535_bin.86_genomic.fna/markers.fasta)
[2023-06-05 05:04:02,304] [INFO] Task started: Blastn
[2023-06-05 05:04:02,304] [INFO] Running command: blastn -query GCA_934320635.1_ERR7738535_bin.86_genomic.fna/markers.fasta -db /var/lib/cwl/stgb52d320e-2373-4b1d-aa98-0fdd2852e45c/dqc_reference/reference_markers_gtdb.fasta -out GCA_934320635.1_ERR7738535_bin.86_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:04:03,072] [INFO] Task succeeded: Blastn
[2023-06-05 05:04:03,076] [INFO] Selected 15 target genomes.
[2023-06-05 05:04:03,076] [INFO] Target genome list was writen to GCA_934320635.1_ERR7738535_bin.86_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:04:03,085] [INFO] Task started: fastANI
[2023-06-05 05:04:03,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg2583a0d9-5838-47f7-a33f-fe7bb3d6741d/GCA_934320635.1_ERR7738535_bin.86_genomic.fna.gz --refList GCA_934320635.1_ERR7738535_bin.86_genomic.fna/target_genomes_gtdb.txt --output GCA_934320635.1_ERR7738535_bin.86_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:04:10,290] [INFO] Task succeeded: fastANI
[2023-06-05 05:04:10,303] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:04:10,304] [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_000153925.1	s__Mediterraneibacter torques	99.6276	641	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.42	99.19	0.88	0.82	25	conclusive
GCA_900556835.1	s__Faecalimonas sp900556835	88.2099	98	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209865.1	s__Mediterraneibacter sp900752395	84.4101	395	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	-
GCF_002159505.1	s__Mediterraneibacter ornithocaccae	78.6703	173	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.93	97.52	0.83	0.82	3	-
GCF_018228665.1	s__UBA9414 sp003458885	78.6368	91	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCF_000155205.1	s__Mediterraneibacter lactaris	78.5958	141	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCF_016902345.1	s__Mediterraneibacter glycyrrhizinilyticus_A	78.1559	125	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113645.1	s__Mediterraneibacter vanvlietii	78.1359	168	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.04	97.81	0.84	0.83	3	-
GCF_008121495.1	s__Ruminococcus_B gnavus	77.9919	161	671	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	-
GCA_019120575.1	s__Mediterraneibacter quadrami	77.6561	120	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116885.1	s__Mediterraneibacter pullistercoris	77.6097	135	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.20	99.20	0.93	0.93	2	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	77.5422	118	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
GCA_019119675.1	s__Mediterraneibacter faecipullorum	77.4335	149	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	77.4004	146	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117305.1	s__Mediterraneibacter merdigallinarum	76.5521	103	671	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 05:04:10,306] [INFO] GTDB search result was written to GCA_934320635.1_ERR7738535_bin.86_genomic.fna/result_gtdb.tsv
[2023-06-05 05:04:10,306] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:04:10,310] [INFO] DFAST_QC result json was written to GCA_934320635.1_ERR7738535_bin.86_genomic.fna/dqc_result.json
[2023-06-05 05:04:10,310] [INFO] DFAST_QC completed!
[2023-06-05 05:04:10,310] [INFO] Total running time: 0h0m45s