[2023-06-27 05:58:06,088] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:58:06,108] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:58:06,108] [INFO] DQC Reference Directory: /var/lib/cwl/stgff3e19ce-1e1c-4b7f-a288-7ad1c638e064/dqc_reference
[2023-06-27 05:58:07,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:58:07,827] [INFO] Task started: Prodigal
[2023-06-27 05:58:07,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg3930d4c2-6a18-442a-a1d4-c3aa84bc18d4/GCA_026003535.1_ASM2600353v1_genomic.fna.gz | prodigal -d GCA_026003535.1_ASM2600353v1_genomic.fna/cds.fna -a GCA_026003535.1_ASM2600353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:58:23,007] [INFO] Task succeeded: Prodigal
[2023-06-27 05:58:23,008] [INFO] Task started: HMMsearch
[2023-06-27 05:58:23,008] [INFO] Running command: hmmsearch --tblout GCA_026003535.1_ASM2600353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff3e19ce-1e1c-4b7f-a288-7ad1c638e064/dqc_reference/reference_markers.hmm GCA_026003535.1_ASM2600353v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:58:23,169] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:58:23,171] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3930d4c2-6a18-442a-a1d4-c3aa84bc18d4/GCA_026003535.1_ASM2600353v1_genomic.fna.gz]
[2023-06-27 05:58:23,212] [INFO] Query marker FASTA was written to GCA_026003535.1_ASM2600353v1_genomic.fna/markers.fasta
[2023-06-27 05:58:23,213] [INFO] Task started: Blastn
[2023-06-27 05:58:23,213] [INFO] Running command: blastn -query GCA_026003535.1_ASM2600353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff3e19ce-1e1c-4b7f-a288-7ad1c638e064/dqc_reference/reference_markers.fasta -out GCA_026003535.1_ASM2600353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:58:26,039] [INFO] Task succeeded: Blastn
[2023-06-27 05:58:26,042] [INFO] Selected 8 target genomes.
[2023-06-27 05:58:26,042] [INFO] Target genome list was writen to GCA_026003535.1_ASM2600353v1_genomic.fna/target_genomes.txt
[2023-06-27 05:58:26,052] [INFO] Task started: fastANI
[2023-06-27 05:58:26,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg3930d4c2-6a18-442a-a1d4-c3aa84bc18d4/GCA_026003535.1_ASM2600353v1_genomic.fna.gz --refList GCA_026003535.1_ASM2600353v1_genomic.fna/target_genomes.txt --output GCA_026003535.1_ASM2600353v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:58:32,873] [INFO] Task succeeded: fastANI
[2023-06-27 05:58:32,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff3e19ce-1e1c-4b7f-a288-7ad1c638e064/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:58:32,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff3e19ce-1e1c-4b7f-a288-7ad1c638e064/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:58:32,881] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-27 05:58:32,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 05:58:32,882] [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
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	98.653	818	865	95	conclusive
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	76.3391	97	865	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	76.3094	163	865	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	76.1907	103	865	95	below_threshold
Rhodothermus profundi	strain=DSM 22212	GCA_900142415.1	633813	633813	type	True	76.1133	54	865	95	below_threshold
Longimonas halophila	strain=KCTC 42399	GCA_002554705.1	1469170	1469170	type	True	75.4851	50	865	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	74.8612	101	865	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:58:32,884] [INFO] DFAST Taxonomy check result was written to GCA_026003535.1_ASM2600353v1_genomic.fna/tc_result.tsv
[2023-06-27 05:58:32,884] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:58:32,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:58:32,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff3e19ce-1e1c-4b7f-a288-7ad1c638e064/dqc_reference/checkm_data
[2023-06-27 05:58:32,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:58:32,914] [INFO] Task started: CheckM
[2023-06-27 05:58:32,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026003535.1_ASM2600353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026003535.1_ASM2600353v1_genomic.fna/checkm_input GCA_026003535.1_ASM2600353v1_genomic.fna/checkm_result
[2023-06-27 05:59:16,393] [INFO] Task succeeded: CheckM
[2023-06-27 05:59:16,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:59:16,420] [INFO] ===== Completeness check finished =====
[2023-06-27 05:59:16,421] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:59:16,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026003535.1_ASM2600353v1_genomic.fna/markers.fasta)
[2023-06-27 05:59:16,421] [INFO] Task started: Blastn
[2023-06-27 05:59:16,421] [INFO] Running command: blastn -query GCA_026003535.1_ASM2600353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff3e19ce-1e1c-4b7f-a288-7ad1c638e064/dqc_reference/reference_markers_gtdb.fasta -out GCA_026003535.1_ASM2600353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:59:17,234] [INFO] Task succeeded: Blastn
[2023-06-27 05:59:17,237] [INFO] Selected 8 target genomes.
[2023-06-27 05:59:17,237] [INFO] Target genome list was writen to GCA_026003535.1_ASM2600353v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:59:17,242] [INFO] Task started: fastANI
[2023-06-27 05:59:17,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg3930d4c2-6a18-442a-a1d4-c3aa84bc18d4/GCA_026003535.1_ASM2600353v1_genomic.fna.gz --refList GCA_026003535.1_ASM2600353v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026003535.1_ASM2600353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:59:22,961] [INFO] Task succeeded: fastANI
[2023-06-27 05:59:22,968] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:59:22,969] [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_011682235.1	s__ISCAR-4553 sp011682235	98.6456	793	865	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__ISCAR-4553;g__ISCAR-4553	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003285105.1	s__MEBICO9517 sp003285105	79.5196	330	865	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__MEBIC09517;g__MEBICO9517	95.0	96.96	96.85	0.95	0.94	3	-
GCF_000024845.1	s__Rhodothermus marinus	77.6453	190	865	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	95.50	95.42	0.92	0.91	8	-
GCA_015487635.1	s__Rhodothermus sp015487635	77.3039	144	865	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rhodothermaceae;g__Rhodothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908885.1	s__JAAAOL01 sp009908885	77.1985	189	865	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643395.1	s__JABDJZ01 sp017643395	76.24	94	865	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__UBA10348;g__JABDJZ01	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002257665.1	s__Rubricoccus marinus	76.2279	104	865	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	76.2054	106	865	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:59:22,971] [INFO] GTDB search result was written to GCA_026003535.1_ASM2600353v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:59:22,971] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:59:22,974] [INFO] DFAST_QC result json was written to GCA_026003535.1_ASM2600353v1_genomic.fna/dqc_result.json
[2023-06-27 05:59:22,974] [INFO] DFAST_QC completed!
[2023-06-27 05:59:22,974] [INFO] Total running time: 0h1m17s