[2023-06-04 17:57:55,718] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:57:55,726] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:57:55,726] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c1f3813-32b9-490b-b21c-03347aa8963a/dqc_reference
[2023-06-04 17:57:56,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:57:56,956] [INFO] Task started: Prodigal
[2023-06-04 17:57:56,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg7220691c-c2c7-493d-9f84-a2c6f4698116/GCA_902805985.1_AVDCRST-MAG01_genomic.fna.gz | prodigal -d GCA_902805985.1_AVDCRST-MAG01_genomic.fna/cds.fna -a GCA_902805985.1_AVDCRST-MAG01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:58:05,992] [INFO] Task succeeded: Prodigal
[2023-06-04 17:58:05,993] [INFO] Task started: HMMsearch
[2023-06-04 17:58:05,993] [INFO] Running command: hmmsearch --tblout GCA_902805985.1_AVDCRST-MAG01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c1f3813-32b9-490b-b21c-03347aa8963a/dqc_reference/reference_markers.hmm GCA_902805985.1_AVDCRST-MAG01_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:58:06,239] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:58:06,241] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7220691c-c2c7-493d-9f84-a2c6f4698116/GCA_902805985.1_AVDCRST-MAG01_genomic.fna.gz]
[2023-06-04 17:58:06,284] [INFO] Query marker FASTA was written to GCA_902805985.1_AVDCRST-MAG01_genomic.fna/markers.fasta
[2023-06-04 17:58:06,284] [INFO] Task started: Blastn
[2023-06-04 17:58:06,284] [INFO] Running command: blastn -query GCA_902805985.1_AVDCRST-MAG01_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c1f3813-32b9-490b-b21c-03347aa8963a/dqc_reference/reference_markers.fasta -out GCA_902805985.1_AVDCRST-MAG01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:58:07,112] [INFO] Task succeeded: Blastn
[2023-06-04 17:58:07,119] [INFO] Selected 11 target genomes.
[2023-06-04 17:58:07,120] [INFO] Target genome list was writen to GCA_902805985.1_AVDCRST-MAG01_genomic.fna/target_genomes.txt
[2023-06-04 17:58:07,304] [INFO] Task started: fastANI
[2023-06-04 17:58:07,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg7220691c-c2c7-493d-9f84-a2c6f4698116/GCA_902805985.1_AVDCRST-MAG01_genomic.fna.gz --refList GCA_902805985.1_AVDCRST-MAG01_genomic.fna/target_genomes.txt --output GCA_902805985.1_AVDCRST-MAG01_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:58:16,685] [INFO] Task succeeded: fastANI
[2023-06-04 17:58:16,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c1f3813-32b9-490b-b21c-03347aa8963a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:58:16,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c1f3813-32b9-490b-b21c-03347aa8963a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:58:16,700] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:58:16,700] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:58:16,700] [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
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	83.5772	643	1051	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	78.9855	387	1051	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	77.7516	236	1051	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	77.7217	235	1051	95	below_threshold
Rubrobacter indicoceani	strain=SCSIO 08198	GCA_003568865.1	2051957	2051957	type	True	77.2364	172	1051	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.3531	108	1051	95	below_threshold
Actinospica robiniae	strain=DSM 44927	GCA_000504285.1	304901	304901	type	True	74.9734	96	1051	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.8642	55	1051	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	74.8291	90	1051	95	below_threshold
Actinospica durhamensis	strain=CSCA 57	GCA_018139695.1	1508375	1508375	type	True	74.7831	88	1051	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:58:16,702] [INFO] DFAST Taxonomy check result was written to GCA_902805985.1_AVDCRST-MAG01_genomic.fna/tc_result.tsv
[2023-06-04 17:58:16,703] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:58:16,703] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:58:16,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c1f3813-32b9-490b-b21c-03347aa8963a/dqc_reference/checkm_data
[2023-06-04 17:58:16,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:58:16,748] [INFO] Task started: CheckM
[2023-06-04 17:58:16,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902805985.1_AVDCRST-MAG01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902805985.1_AVDCRST-MAG01_genomic.fna/checkm_input GCA_902805985.1_AVDCRST-MAG01_genomic.fna/checkm_result
[2023-06-04 17:58:46,465] [INFO] Task succeeded: CheckM
[2023-06-04 17:58:46,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-04 17:58:46,490] [INFO] ===== Completeness check finished =====
[2023-06-04 17:58:46,490] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:58:46,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902805985.1_AVDCRST-MAG01_genomic.fna/markers.fasta)
[2023-06-04 17:58:46,491] [INFO] Task started: Blastn
[2023-06-04 17:58:46,491] [INFO] Running command: blastn -query GCA_902805985.1_AVDCRST-MAG01_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c1f3813-32b9-490b-b21c-03347aa8963a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902805985.1_AVDCRST-MAG01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:58:47,497] [INFO] Task succeeded: Blastn
[2023-06-04 17:58:47,502] [INFO] Selected 8 target genomes.
[2023-06-04 17:58:47,502] [INFO] Target genome list was writen to GCA_902805985.1_AVDCRST-MAG01_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:58:47,606] [INFO] Task started: fastANI
[2023-06-04 17:58:47,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg7220691c-c2c7-493d-9f84-a2c6f4698116/GCA_902805985.1_AVDCRST-MAG01_genomic.fna.gz --refList GCA_902805985.1_AVDCRST-MAG01_genomic.fna/target_genomes_gtdb.txt --output GCA_902805985.1_AVDCRST-MAG01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:58:54,083] [INFO] Task succeeded: fastANI
[2023-06-04 17:58:54,098] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:58:54,098] [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_902805985.1	s__SCSIO-52909 sp902805985	100.0	1027	1051	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902805975.1	s__SCSIO-52909 sp902805975	89.8472	617	1051	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806085.1	s__SCSIO-52909 sp902806085	85.5201	697	1051	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815575.1	s__SCSIO-52909 sp013815575	83.8015	376	1051	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	97.69	97.69	0.64	0.64	2	-
GCF_011492945.1	s__SCSIO-52909 sp011492945	83.5915	642	1051	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806015.1	s__SCSIO-52909 sp902806015	83.0124	471	1051	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781725.1	s__SCSIO-52909 sp016781725	80.2379	303	1051	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	98.84	98.84	0.72	0.72	2	-
GCF_000014185.1	s__Rubrobacter_B xylanophilus	78.1258	302	1051	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:58:54,100] [INFO] GTDB search result was written to GCA_902805985.1_AVDCRST-MAG01_genomic.fna/result_gtdb.tsv
[2023-06-04 17:58:54,101] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:58:54,104] [INFO] DFAST_QC result json was written to GCA_902805985.1_AVDCRST-MAG01_genomic.fna/dqc_result.json
[2023-06-04 17:58:54,105] [INFO] DFAST_QC completed!
[2023-06-04 17:58:54,105] [INFO] Total running time: 0h0m58s