[2023-06-18 20:56:22,649] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:22,652] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:22,652] [INFO] DQC Reference Directory: /var/lib/cwl/stgabd054ea-75d6-424f-9fba-6477c5949aa9/dqc_reference
[2023-06-18 20:56:23,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:23,979] [INFO] Task started: Prodigal
[2023-06-18 20:56:23,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg48e9ecf5-31a0-42e9-90bf-3201ead5e04a/GCA_018267495.1_ASM1826749v1_genomic.fna.gz | prodigal -d GCA_018267495.1_ASM1826749v1_genomic.fna/cds.fna -a GCA_018267495.1_ASM1826749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:37,474] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:37,475] [INFO] Task started: HMMsearch
[2023-06-18 20:56:37,475] [INFO] Running command: hmmsearch --tblout GCA_018267495.1_ASM1826749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabd054ea-75d6-424f-9fba-6477c5949aa9/dqc_reference/reference_markers.hmm GCA_018267495.1_ASM1826749v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:37,748] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:37,749] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg48e9ecf5-31a0-42e9-90bf-3201ead5e04a/GCA_018267495.1_ASM1826749v1_genomic.fna.gz]
[2023-06-18 20:56:37,784] [INFO] Query marker FASTA was written to GCA_018267495.1_ASM1826749v1_genomic.fna/markers.fasta
[2023-06-18 20:56:37,785] [INFO] Task started: Blastn
[2023-06-18 20:56:37,785] [INFO] Running command: blastn -query GCA_018267495.1_ASM1826749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd054ea-75d6-424f-9fba-6477c5949aa9/dqc_reference/reference_markers.fasta -out GCA_018267495.1_ASM1826749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:38,422] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:38,426] [INFO] Selected 26 target genomes.
[2023-06-18 20:56:38,426] [INFO] Target genome list was writen to GCA_018267495.1_ASM1826749v1_genomic.fna/target_genomes.txt
[2023-06-18 20:56:38,430] [INFO] Task started: fastANI
[2023-06-18 20:56:38,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e9ecf5-31a0-42e9-90bf-3201ead5e04a/GCA_018267495.1_ASM1826749v1_genomic.fna.gz --refList GCA_018267495.1_ASM1826749v1_genomic.fna/target_genomes.txt --output GCA_018267495.1_ASM1826749v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:57:02,294] [INFO] Task succeeded: fastANI
[2023-06-18 20:57:02,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabd054ea-75d6-424f-9fba-6477c5949aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:57:02,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabd054ea-75d6-424f-9fba-6477c5949aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:57:02,301] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:57:02,302] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:57:02,302] [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
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.6849	63	941	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:57:02,304] [INFO] DFAST Taxonomy check result was written to GCA_018267495.1_ASM1826749v1_genomic.fna/tc_result.tsv
[2023-06-18 20:57:02,305] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:57:02,305] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:57:02,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabd054ea-75d6-424f-9fba-6477c5949aa9/dqc_reference/checkm_data
[2023-06-18 20:57:02,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:57:02,348] [INFO] Task started: CheckM
[2023-06-18 20:57:02,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018267495.1_ASM1826749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018267495.1_ASM1826749v1_genomic.fna/checkm_input GCA_018267495.1_ASM1826749v1_genomic.fna/checkm_result
[2023-06-18 20:57:46,556] [INFO] Task succeeded: CheckM
[2023-06-18 20:57:46,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 16.67%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:57:46,588] [INFO] ===== Completeness check finished =====
[2023-06-18 20:57:46,589] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:57:46,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018267495.1_ASM1826749v1_genomic.fna/markers.fasta)
[2023-06-18 20:57:46,589] [INFO] Task started: Blastn
[2023-06-18 20:57:46,589] [INFO] Running command: blastn -query GCA_018267495.1_ASM1826749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabd054ea-75d6-424f-9fba-6477c5949aa9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018267495.1_ASM1826749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:57:47,508] [INFO] Task succeeded: Blastn
[2023-06-18 20:57:47,513] [INFO] Selected 19 target genomes.
[2023-06-18 20:57:47,513] [INFO] Target genome list was writen to GCA_018267495.1_ASM1826749v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:57:47,521] [INFO] Task started: fastANI
[2023-06-18 20:57:47,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e9ecf5-31a0-42e9-90bf-3201ead5e04a/GCA_018267495.1_ASM1826749v1_genomic.fna.gz --refList GCA_018267495.1_ASM1826749v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018267495.1_ASM1826749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:57:58,926] [INFO] Task succeeded: fastANI
[2023-06-18 20:57:58,951] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:57:58,951] [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_018267515.1	s__UTBCD1 sp018267515	99.8052	650	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UTBCD1	95.0	99.81	99.81	0.71	0.71	2	conclusive
GCA_002069045.1	s__JJ008 sp002069045	78.7225	68	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266555.1	s__UTBCD1 sp018266555	77.8666	342	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UTBCD1	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002066995.1	s__UTBCD1 sp002066995	77.0974	268	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UTBCD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352145.1	s__JJ008 sp002352145	76.3778	72	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786885.1	s__JJ008 sp016786885	76.3755	84	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235125.1	s__JJ008 sp016235125	76.1651	120	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185185.1	s__AWTP1-9 sp016185185	76.0465	60	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400415.1	s__JJ008 sp002400415	75.9661	98	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882315.1	s__VBAR01 sp005882315	75.9375	99	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267535.1	s__JAFDYH01 sp018267535	75.6673	90	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFDYH01	95.0	98.33	98.33	0.81	0.81	2	-
GCA_016786805.1	s__JJ008 sp016786805	75.6631	63	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882975.1	s__VBAS01 sp005882975	75.6348	104	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870685.1	s__CAILAF01 sp903870685	75.4306	52	941	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.70	99.46	0.92	0.91	5	-
--------------------------------------------------------------------------------
[2023-06-18 20:57:58,954] [INFO] GTDB search result was written to GCA_018267495.1_ASM1826749v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:57:58,955] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:57:58,958] [INFO] DFAST_QC result json was written to GCA_018267495.1_ASM1826749v1_genomic.fna/dqc_result.json
[2023-06-18 20:57:58,959] [INFO] DFAST_QC completed!
[2023-06-18 20:57:58,959] [INFO] Total running time: 0h1m36s