[2024-01-24 13:31:34,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:34,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:34,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg270bf2c2-bdd7-48b2-aac5-e72d4cd765bd/dqc_reference
[2024-01-24 13:31:36,326] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,327] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a5a626b-7d21-4edd-a913-bc6b1841ce55/GCF_003987475.1_ASM398747v1_genomic.fna.gz | prodigal -d GCF_003987475.1_ASM398747v1_genomic.fna/cds.fna -a GCF_003987475.1_ASM398747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:43,431] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:43,432] [INFO] Task started: HMMsearch
[2024-01-24 13:31:43,432] [INFO] Running command: hmmsearch --tblout GCF_003987475.1_ASM398747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg270bf2c2-bdd7-48b2-aac5-e72d4cd765bd/dqc_reference/reference_markers.hmm GCF_003987475.1_ASM398747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:43,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:43,727] [INFO] Found 6/6 markers.
[2024-01-24 13:31:43,755] [INFO] Query marker FASTA was written to GCF_003987475.1_ASM398747v1_genomic.fna/markers.fasta
[2024-01-24 13:31:43,756] [INFO] Task started: Blastn
[2024-01-24 13:31:43,756] [INFO] Running command: blastn -query GCF_003987475.1_ASM398747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg270bf2c2-bdd7-48b2-aac5-e72d4cd765bd/dqc_reference/reference_markers.fasta -out GCF_003987475.1_ASM398747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:44,630] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:44,633] [INFO] Selected 27 target genomes.
[2024-01-24 13:31:44,633] [INFO] Target genome list was writen to GCF_003987475.1_ASM398747v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:44,671] [INFO] Task started: fastANI
[2024-01-24 13:31:44,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a5a626b-7d21-4edd-a913-bc6b1841ce55/GCF_003987475.1_ASM398747v1_genomic.fna.gz --refList GCF_003987475.1_ASM398747v1_genomic.fna/target_genomes.txt --output GCF_003987475.1_ASM398747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:58,895] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:58,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg270bf2c2-bdd7-48b2-aac5-e72d4cd765bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:58,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg270bf2c2-bdd7-48b2-aac5-e72d4cd765bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:58,911] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:58,911] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:58,911] [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
Idiomarina tyrosinivorans	strain=CC-PW-9	GCA_003987475.1	1445662	1445662	type	True	100.0	795	799	95	conclusive
Idiomarina baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	79.5605	99	799	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	79.1978	108	799	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	79.0544	122	799	95	below_threshold
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	78.9245	78	799	95	below_threshold
Pseudidiomarina homiensis	strain=PO-M2	GCA_003987225.1	364198	364198	type	True	78.7979	88	799	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	78.7877	92	799	95	below_threshold
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	78.7837	97	799	95	below_threshold
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	78.337	115	799	95	below_threshold
Idiomarina fontislapidosi	strain=CECT 5859	GCA_003226255.1	263723	263723	type	True	78.2331	114	799	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	78.1647	84	799	95	below_threshold
Pseudidiomarina planktonica	strain=TS-T11	GCA_003987425.1	1323738	1323738	type	True	77.8844	88	799	95	below_threshold
Pseudidiomarina planktonica	strain=CGMCC 1.12458	GCA_900177775.1	1323738	1323738	type	True	77.8325	88	799	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	77.371	54	799	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	77.0861	52	799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:58,913] [INFO] DFAST Taxonomy check result was written to GCF_003987475.1_ASM398747v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:58,913] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:58,913] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:58,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg270bf2c2-bdd7-48b2-aac5-e72d4cd765bd/dqc_reference/checkm_data
[2024-01-24 13:31:58,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:58,958] [INFO] Task started: CheckM
[2024-01-24 13:31:58,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987475.1_ASM398747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987475.1_ASM398747v1_genomic.fna/checkm_input GCF_003987475.1_ASM398747v1_genomic.fna/checkm_result
[2024-01-24 13:32:25,119] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:25,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,137] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:25,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:25,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987475.1_ASM398747v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:25,139] [INFO] Task started: Blastn
[2024-01-24 13:32:25,139] [INFO] Running command: blastn -query GCF_003987475.1_ASM398747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg270bf2c2-bdd7-48b2-aac5-e72d4cd765bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987475.1_ASM398747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:26,281] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:26,284] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:26,285] [INFO] Target genome list was writen to GCF_003987475.1_ASM398747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:26,322] [INFO] Task started: fastANI
[2024-01-24 13:32:26,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a5a626b-7d21-4edd-a913-bc6b1841ce55/GCF_003987475.1_ASM398747v1_genomic.fna.gz --refList GCF_003987475.1_ASM398747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987475.1_ASM398747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:38,201] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:38,216] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:38,216] [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_003987475.1	s__Idiomarina tyrosinivorans	100.0	795	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000152885.1	s__Idiomarina baltica	79.5424	100	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	98.48	98.19	0.90	0.79	8	-
GCF_004362895.1	s__Idiomarina sp002729675	79.1629	112	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_000008465.1	s__Idiomarina loihiensis	79.0544	122	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	79.0503	94	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806985.1	s__Pseudidiomarina piscicola	78.9231	78	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	78.8206	106	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_003987225.1	s__Pseudidiomarina homiensis	78.7979	88	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987095.1	s__Idiomarina piscisalsi	78.7877	92	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870515.1	s__Idiomarina sp001870515	78.5787	107	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226255.1	s__Idiomarina fontislapidosi	78.3009	112	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987045.1	s__Pseudidiomarina marina	78.1647	84	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCA_002685255.1	s__Idiomarina sp002685255	78.0366	88	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.23	98.54	0.93	0.91	3	-
GCF_900177775.1	s__Pseudidiomarina planktonica	77.8328	90	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007096385.1	s__Aliidiomarina sp007096385	77.371	54	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987135.1	s__Aliidiomarina iranensis	77.3344	58	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423905.1	s__Pseudidiomarina sp002423905	77.0386	51	799	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:38,220] [INFO] GTDB search result was written to GCF_003987475.1_ASM398747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:38,222] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:38,228] [INFO] DFAST_QC result json was written to GCF_003987475.1_ASM398747v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:38,228] [INFO] DFAST_QC completed!
[2024-01-24 13:32:38,228] [INFO] Total running time: 0h1m3s