[2024-01-24 12:07:18,966] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:18,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:18,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg104556ee-b1c2-4313-b9df-678efe6296dd/dqc_reference
[2024-01-24 12:07:20,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:20,153] [INFO] Task started: Prodigal
[2024-01-24 12:07:20,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg67d43344-43b2-45ae-9950-bf0ef5ae7bab/GCF_002257665.1_ASM225766v1_genomic.fna.gz | prodigal -d GCF_002257665.1_ASM225766v1_genomic.fna/cds.fna -a GCF_002257665.1_ASM225766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:44,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:44,908] [INFO] Task started: HMMsearch
[2024-01-24 12:07:44,908] [INFO] Running command: hmmsearch --tblout GCF_002257665.1_ASM225766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg104556ee-b1c2-4313-b9df-678efe6296dd/dqc_reference/reference_markers.hmm GCF_002257665.1_ASM225766v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:45,193] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:45,196] [INFO] Found 6/6 markers.
[2024-01-24 12:07:45,236] [INFO] Query marker FASTA was written to GCF_002257665.1_ASM225766v1_genomic.fna/markers.fasta
[2024-01-24 12:07:45,237] [INFO] Task started: Blastn
[2024-01-24 12:07:45,237] [INFO] Running command: blastn -query GCF_002257665.1_ASM225766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg104556ee-b1c2-4313-b9df-678efe6296dd/dqc_reference/reference_markers.fasta -out GCF_002257665.1_ASM225766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:45,966] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:45,971] [INFO] Selected 21 target genomes.
[2024-01-24 12:07:45,971] [INFO] Target genome list was writen to GCF_002257665.1_ASM225766v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:45,980] [INFO] Task started: fastANI
[2024-01-24 12:07:45,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d43344-43b2-45ae-9950-bf0ef5ae7bab/GCF_002257665.1_ASM225766v1_genomic.fna.gz --refList GCF_002257665.1_ASM225766v1_genomic.fna/target_genomes.txt --output GCF_002257665.1_ASM225766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:08:01,850] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:01,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg104556ee-b1c2-4313-b9df-678efe6296dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:08:01,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg104556ee-b1c2-4313-b9df-678efe6296dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:08:01,872] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:08:01,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:08:01,872] [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
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	100.0	1469	1471	95	conclusive
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	78.1802	551	1471	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	76.4286	171	1471	95	below_threshold
Salisaeta longa	strain=DSM 21114	GCA_000419585.1	503170	503170	type	True	75.9786	73	1471	95	below_threshold
Salinibacter ruber	strain=DSM 13855; M31	GCA_000013045.1	146919	146919	type	True	75.7373	88	1471	95	below_threshold
Longibacter salinarum	strain=KCTC 52045	GCA_002554795.1	1850348	1850348	type	True	75.4262	58	1471	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	75.1701	57	1471	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	75.1625	72	1471	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	75.1597	58	1471	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.1292	69	1471	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	75.1145	72	1471	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	75.1096	52	1471	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	74.9488	97	1471	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	74.9429	95	1471	95	below_threshold
Methylobacterium durans	strain=17SD2-17	GCA_003173715.1	2202825	2202825	type	True	74.9407	114	1471	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	74.9398	93	1471	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	74.9185	97	1471	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.914	137	1471	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.8878	186	1471	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	74.8271	145	1471	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.8094	233	1471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:08:01,874] [INFO] DFAST Taxonomy check result was written to GCF_002257665.1_ASM225766v1_genomic.fna/tc_result.tsv
[2024-01-24 12:08:01,875] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:08:01,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:08:01,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg104556ee-b1c2-4313-b9df-678efe6296dd/dqc_reference/checkm_data
[2024-01-24 12:08:01,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:08:01,922] [INFO] Task started: CheckM
[2024-01-24 12:08:01,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002257665.1_ASM225766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002257665.1_ASM225766v1_genomic.fna/checkm_input GCF_002257665.1_ASM225766v1_genomic.fna/checkm_result
[2024-01-24 12:09:05,033] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:05,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:05,058] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:05,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:05,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002257665.1_ASM225766v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:05,059] [INFO] Task started: Blastn
[2024-01-24 12:09:05,059] [INFO] Running command: blastn -query GCF_002257665.1_ASM225766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg104556ee-b1c2-4313-b9df-678efe6296dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002257665.1_ASM225766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:06,086] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:06,090] [INFO] Selected 9 target genomes.
[2024-01-24 12:09:06,091] [INFO] Target genome list was writen to GCF_002257665.1_ASM225766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:06,098] [INFO] Task started: fastANI
[2024-01-24 12:09:06,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d43344-43b2-45ae-9950-bf0ef5ae7bab/GCF_002257665.1_ASM225766v1_genomic.fna.gz --refList GCF_002257665.1_ASM225766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002257665.1_ASM225766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:13,634] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:13,644] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:13,644] [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_002257665.1	s__Rubricoccus marinus	100.0	1469	1471	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012960515.1	s__Rubricoccus sp012960515	80.4179	658	1471	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	78.6884	578	1471	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCF_002283365.1	s__Rubrivirga marina	78.1551	555	1471	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	77.9054	377	1471	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003465.1	s__JABDIZ01 sp013003465	77.6324	246	1471	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__JABDIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908885.1	s__JAAAOL01 sp009908885	76.506	166	1471	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Salinibacteraceae;g__JAAAOL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:13,646] [INFO] GTDB search result was written to GCF_002257665.1_ASM225766v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:13,647] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:13,651] [INFO] DFAST_QC result json was written to GCF_002257665.1_ASM225766v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:13,651] [INFO] DFAST_QC completed!
[2024-01-24 12:09:13,651] [INFO] Total running time: 0h1m55s