[2023-06-30 17:54:04,972] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:54:04,974] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:54:04,975] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0b5a2d8-0498-4ea3-864e-ad261f6658fe/dqc_reference
[2023-06-30 17:54:06,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:54:06,145] [INFO] Task started: Prodigal
[2023-06-30 17:54:06,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg55bb5dbb-f4d1-4c5e-8422-fa1282ccccc7/GCA_900752245.1_ERS235568_37_genomic.fna.gz | prodigal -d GCA_900752245.1_ERS235568_37_genomic.fna/cds.fna -a GCA_900752245.1_ERS235568_37_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:54:09,854] [INFO] Task succeeded: Prodigal
[2023-06-30 17:54:09,854] [INFO] Task started: HMMsearch
[2023-06-30 17:54:09,854] [INFO] Running command: hmmsearch --tblout GCA_900752245.1_ERS235568_37_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0b5a2d8-0498-4ea3-864e-ad261f6658fe/dqc_reference/reference_markers.hmm GCA_900752245.1_ERS235568_37_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:54:10,025] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:54:10,027] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg55bb5dbb-f4d1-4c5e-8422-fa1282ccccc7/GCA_900752245.1_ERS235568_37_genomic.fna.gz]
[2023-06-30 17:54:10,048] [INFO] Query marker FASTA was written to GCA_900752245.1_ERS235568_37_genomic.fna/markers.fasta
[2023-06-30 17:54:10,048] [INFO] Task started: Blastn
[2023-06-30 17:54:10,048] [INFO] Running command: blastn -query GCA_900752245.1_ERS235568_37_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0b5a2d8-0498-4ea3-864e-ad261f6658fe/dqc_reference/reference_markers.fasta -out GCA_900752245.1_ERS235568_37_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:54:10,621] [INFO] Task succeeded: Blastn
[2023-06-30 17:54:10,626] [INFO] Selected 23 target genomes.
[2023-06-30 17:54:10,627] [INFO] Target genome list was writen to GCA_900752245.1_ERS235568_37_genomic.fna/target_genomes.txt
[2023-06-30 17:54:10,628] [INFO] Task started: fastANI
[2023-06-30 17:54:10,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg55bb5dbb-f4d1-4c5e-8422-fa1282ccccc7/GCA_900752245.1_ERS235568_37_genomic.fna.gz --refList GCA_900752245.1_ERS235568_37_genomic.fna/target_genomes.txt --output GCA_900752245.1_ERS235568_37_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:54:19,852] [INFO] Task succeeded: fastANI
[2023-06-30 17:54:19,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0b5a2d8-0498-4ea3-864e-ad261f6658fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:54:19,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0b5a2d8-0498-4ea3-864e-ad261f6658fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:54:19,860] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:54:19,861] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:54:19,861] [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	87.5219	76	211	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	87.3423	77	211	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	86.8851	113	211	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	86.706	84	211	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	86.5696	85	211	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	82.264	68	211	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	81.5463	81	211	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.7164	54	211	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:54:19,863] [INFO] DFAST Taxonomy check result was written to GCA_900752245.1_ERS235568_37_genomic.fna/tc_result.tsv
[2023-06-30 17:54:19,863] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:54:19,863] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:54:19,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0b5a2d8-0498-4ea3-864e-ad261f6658fe/dqc_reference/checkm_data
[2023-06-30 17:54:19,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:54:19,887] [INFO] Task started: CheckM
[2023-06-30 17:54:19,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900752245.1_ERS235568_37_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900752245.1_ERS235568_37_genomic.fna/checkm_input GCA_900752245.1_ERS235568_37_genomic.fna/checkm_result
[2023-06-30 17:54:38,574] [INFO] Task succeeded: CheckM
[2023-06-30 17:54:38,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.77%
Contamintation: 17.05%
Strain heterogeneity: 70.45%
--------------------------------------------------------------------------------
[2023-06-30 17:54:38,599] [INFO] ===== Completeness check finished =====
[2023-06-30 17:54:38,599] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:54:38,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900752245.1_ERS235568_37_genomic.fna/markers.fasta)
[2023-06-30 17:54:38,600] [INFO] Task started: Blastn
[2023-06-30 17:54:38,600] [INFO] Running command: blastn -query GCA_900752245.1_ERS235568_37_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0b5a2d8-0498-4ea3-864e-ad261f6658fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_900752245.1_ERS235568_37_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:54:39,354] [INFO] Task succeeded: Blastn
[2023-06-30 17:54:39,359] [INFO] Selected 22 target genomes.
[2023-06-30 17:54:39,359] [INFO] Target genome list was writen to GCA_900752245.1_ERS235568_37_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:54:39,362] [INFO] Task started: fastANI
[2023-06-30 17:54:39,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg55bb5dbb-f4d1-4c5e-8422-fa1282ccccc7/GCA_900752245.1_ERS235568_37_genomic.fna.gz --refList GCA_900752245.1_ERS235568_37_genomic.fna/target_genomes_gtdb.txt --output GCA_900752245.1_ERS235568_37_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:54:49,709] [INFO] Task succeeded: fastANI
[2023-06-30 17:54:49,719] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 17:54:49,719] [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	87.5219	76	211	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_000484655.1	s__Blautia_A wexlerae	86.5696	85	211	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_013300825.1	s__Blautia_A wexlerae_B	85.9349	83	211	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	-
GCF_003477525.1	s__Blautia_A sp003477525	82.1544	74	211	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCF_000210015.1	s__Blautia_A obeum_B	81.7594	70	211	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_009707925.1	s__Blautia_A luti	81.6355	80	211	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCF_900120195.1	s__Blautia_A sp900120195	80.5417	76	211	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	-
GCA_905209435.1	s__Blautia_A sp905209435	80.4537	71	211	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	-
GCF_018918125.1	s__Blautia_A sp018918125	80.1835	73	211	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_900551715.1	s__Blautia_A sp900551715	77.6216	64	211	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	-
--------------------------------------------------------------------------------
[2023-06-30 17:54:49,721] [INFO] GTDB search result was written to GCA_900752245.1_ERS235568_37_genomic.fna/result_gtdb.tsv
[2023-06-30 17:54:49,722] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:54:49,725] [INFO] DFAST_QC result json was written to GCA_900752245.1_ERS235568_37_genomic.fna/dqc_result.json
[2023-06-30 17:54:49,726] [INFO] DFAST_QC completed!
[2023-06-30 17:54:49,726] [INFO] Total running time: 0h0m45s