[2023-06-05 05:36:42,579] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:36:42,586] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:36:42,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg8502be5b-7aad-4c4b-92ca-b9638e795af6/dqc_reference
[2023-06-05 05:36:44,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:36:44,686] [INFO] Task started: Prodigal
[2023-06-05 05:36:44,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg6558be30-e0f5-41ce-8b04-4cc49ff00887/GCA_934372025.1_ERR7738660_bin.238_genomic.fna.gz | prodigal -d GCA_934372025.1_ERR7738660_bin.238_genomic.fna/cds.fna -a GCA_934372025.1_ERR7738660_bin.238_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:36:51,033] [INFO] Task succeeded: Prodigal
[2023-06-05 05:36:51,034] [INFO] Task started: HMMsearch
[2023-06-05 05:36:51,034] [INFO] Running command: hmmsearch --tblout GCA_934372025.1_ERR7738660_bin.238_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8502be5b-7aad-4c4b-92ca-b9638e795af6/dqc_reference/reference_markers.hmm GCA_934372025.1_ERR7738660_bin.238_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:36:51,374] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:36:51,375] [INFO] Found 6/6 markers.
[2023-06-05 05:36:51,408] [INFO] Query marker FASTA was written to GCA_934372025.1_ERR7738660_bin.238_genomic.fna/markers.fasta
[2023-06-05 05:36:51,408] [INFO] Task started: Blastn
[2023-06-05 05:36:51,409] [INFO] Running command: blastn -query GCA_934372025.1_ERR7738660_bin.238_genomic.fna/markers.fasta -db /var/lib/cwl/stg8502be5b-7aad-4c4b-92ca-b9638e795af6/dqc_reference/reference_markers.fasta -out GCA_934372025.1_ERR7738660_bin.238_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:36:52,117] [INFO] Task succeeded: Blastn
[2023-06-05 05:36:52,173] [INFO] Selected 14 target genomes.
[2023-06-05 05:36:52,174] [INFO] Target genome list was writen to GCA_934372025.1_ERR7738660_bin.238_genomic.fna/target_genomes.txt
[2023-06-05 05:36:52,175] [INFO] Task started: fastANI
[2023-06-05 05:36:52,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg6558be30-e0f5-41ce-8b04-4cc49ff00887/GCA_934372025.1_ERR7738660_bin.238_genomic.fna.gz --refList GCA_934372025.1_ERR7738660_bin.238_genomic.fna/target_genomes.txt --output GCA_934372025.1_ERR7738660_bin.238_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:37:01,709] [INFO] Task succeeded: fastANI
[2023-06-05 05:37:01,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8502be5b-7aad-4c4b-92ca-b9638e795af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:37:01,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8502be5b-7aad-4c4b-92ca-b9638e795af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:37:01,729] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:37:01,729] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 05:37:01,729] [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
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	84.7854	570	807	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	84.7121	585	807	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	82.3105	510	807	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.5168	275	807	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.4486	269	807	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.2694	243	807	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.0902	240	807	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.5313	251	807	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.456	98	807	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.0527	72	807	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.769	91	807	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.7313	88	807	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	76.3515	71	807	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 05:37:01,731] [INFO] DFAST Taxonomy check result was written to GCA_934372025.1_ERR7738660_bin.238_genomic.fna/tc_result.tsv
[2023-06-05 05:37:01,732] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:37:01,732] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:37:01,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8502be5b-7aad-4c4b-92ca-b9638e795af6/dqc_reference/checkm_data
[2023-06-05 05:37:01,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:37:01,791] [INFO] Task started: CheckM
[2023-06-05 05:37:01,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934372025.1_ERR7738660_bin.238_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934372025.1_ERR7738660_bin.238_genomic.fna/checkm_input GCA_934372025.1_ERR7738660_bin.238_genomic.fna/checkm_result
[2023-06-05 05:37:29,284] [INFO] Task succeeded: CheckM
[2023-06-05 05:37:29,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:37:29,307] [INFO] ===== Completeness check finished =====
[2023-06-05 05:37:29,308] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:37:29,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934372025.1_ERR7738660_bin.238_genomic.fna/markers.fasta)
[2023-06-05 05:37:29,309] [INFO] Task started: Blastn
[2023-06-05 05:37:29,309] [INFO] Running command: blastn -query GCA_934372025.1_ERR7738660_bin.238_genomic.fna/markers.fasta -db /var/lib/cwl/stg8502be5b-7aad-4c4b-92ca-b9638e795af6/dqc_reference/reference_markers_gtdb.fasta -out GCA_934372025.1_ERR7738660_bin.238_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:37:30,405] [INFO] Task succeeded: Blastn
[2023-06-05 05:37:30,410] [INFO] Selected 10 target genomes.
[2023-06-05 05:37:30,410] [INFO] Target genome list was writen to GCA_934372025.1_ERR7738660_bin.238_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:37:30,414] [INFO] Task started: fastANI
[2023-06-05 05:37:30,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg6558be30-e0f5-41ce-8b04-4cc49ff00887/GCA_934372025.1_ERR7738660_bin.238_genomic.fna.gz --refList GCA_934372025.1_ERR7738660_bin.238_genomic.fna/target_genomes_gtdb.txt --output GCA_934372025.1_ERR7738660_bin.238_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:37:36,573] [INFO] Task succeeded: fastANI
[2023-06-05 05:37:36,586] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 05:37:36,586] [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_000153905.1	s__Blautia_A obeum	84.7933	568	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.25	97.20	0.82	0.75	45	-
GCF_018918125.1	s__Blautia_A sp018918125	83.1889	506	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900066355.1	s__Blautia_A sp900066355	82.5719	487	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.38	98.38	0.93	0.93	2	-
GCF_009883055.1	s__Blautia_A sp900548245	82.485	474	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.63	98.37	0.88	0.85	5	-
GCF_900120195.1	s__Blautia_A sp900120195	82.3917	510	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.52	98.42	0.85	0.83	5	-
GCF_000210015.1	s__Blautia_A obeum_B	82.3794	515	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.64	98.44	0.85	0.84	7	-
GCF_003461245.1	s__Blautia_A sp000436615	81.5901	463	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.75	98.36	0.88	0.81	8	-
GCA_900551715.1	s__Blautia_A sp900551715	80.2169	350	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900751995.1	s__Blautia_A sp900751995	80.1007	208	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	95.05	95.05	0.55	0.55	2	-
GCF_013300825.1	s__Blautia_A wexlerae_B	79.2874	259	807	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
--------------------------------------------------------------------------------
[2023-06-05 05:37:36,588] [INFO] GTDB search result was written to GCA_934372025.1_ERR7738660_bin.238_genomic.fna/result_gtdb.tsv
[2023-06-05 05:37:36,589] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:37:36,592] [INFO] DFAST_QC result json was written to GCA_934372025.1_ERR7738660_bin.238_genomic.fna/dqc_result.json
[2023-06-05 05:37:36,592] [INFO] DFAST_QC completed!
[2023-06-05 05:37:36,592] [INFO] Total running time: 0h0m54s