[2024-01-25 20:24:05,672] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:24:05,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:24:05,674] [INFO] DQC Reference Directory: /var/lib/cwl/stgefae244d-b0a5-4053-83e0-a730621b0c4d/dqc_reference
[2024-01-25 20:24:06,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:24:06,811] [INFO] Task started: Prodigal
[2024-01-25 20:24:06,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg74e601b1-7d82-4631-9e2f-014fe3809ed1/GCF_024159085.1_ASM2415908v1_genomic.fna.gz | prodigal -d GCF_024159085.1_ASM2415908v1_genomic.fna/cds.fna -a GCF_024159085.1_ASM2415908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:12,702] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:12,703] [INFO] Task started: HMMsearch
[2024-01-25 20:24:12,703] [INFO] Running command: hmmsearch --tblout GCF_024159085.1_ASM2415908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefae244d-b0a5-4053-83e0-a730621b0c4d/dqc_reference/reference_markers.hmm GCF_024159085.1_ASM2415908v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:12,901] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:12,902] [INFO] Found 6/6 markers.
[2024-01-25 20:24:12,928] [INFO] Query marker FASTA was written to GCF_024159085.1_ASM2415908v1_genomic.fna/markers.fasta
[2024-01-25 20:24:12,928] [INFO] Task started: Blastn
[2024-01-25 20:24:12,928] [INFO] Running command: blastn -query GCF_024159085.1_ASM2415908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefae244d-b0a5-4053-83e0-a730621b0c4d/dqc_reference/reference_markers.fasta -out GCF_024159085.1_ASM2415908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:13,596] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:13,598] [INFO] Selected 12 target genomes.
[2024-01-25 20:24:13,599] [INFO] Target genome list was writen to GCF_024159085.1_ASM2415908v1_genomic.fna/target_genomes.txt
[2024-01-25 20:24:13,605] [INFO] Task started: fastANI
[2024-01-25 20:24:13,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e601b1-7d82-4631-9e2f-014fe3809ed1/GCF_024159085.1_ASM2415908v1_genomic.fna.gz --refList GCF_024159085.1_ASM2415908v1_genomic.fna/target_genomes.txt --output GCF_024159085.1_ASM2415908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:20,900] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:20,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefae244d-b0a5-4053-83e0-a730621b0c4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:20,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefae244d-b0a5-4053-83e0-a730621b0c4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:20,906] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:24:20,906] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:24:20,907] [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 loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	93.3571	830	951	95	below_threshold
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	84.4967	657	951	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	84.153	636	951	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	84.0759	659	951	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	80.2547	383	951	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	80.1731	357	951	95	below_threshold
Idiomarina mangrovi	strain=ZQ330	GCA_003999375.1	2487133	2487133	type	True	77.3821	83	951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:20,908] [INFO] DFAST Taxonomy check result was written to GCF_024159085.1_ASM2415908v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:20,908] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:20,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:20,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefae244d-b0a5-4053-83e0-a730621b0c4d/dqc_reference/checkm_data
[2024-01-25 20:24:20,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:20,942] [INFO] Task started: CheckM
[2024-01-25 20:24:20,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024159085.1_ASM2415908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024159085.1_ASM2415908v1_genomic.fna/checkm_input GCF_024159085.1_ASM2415908v1_genomic.fna/checkm_result
[2024-01-25 20:24:43,689] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:43,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:43,705] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:43,705] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:43,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024159085.1_ASM2415908v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:43,705] [INFO] Task started: Blastn
[2024-01-25 20:24:43,705] [INFO] Running command: blastn -query GCF_024159085.1_ASM2415908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefae244d-b0a5-4053-83e0-a730621b0c4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024159085.1_ASM2415908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:44,892] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:44,897] [INFO] Selected 9 target genomes.
[2024-01-25 20:24:44,897] [INFO] Target genome list was writen to GCF_024159085.1_ASM2415908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:44,934] [INFO] Task started: fastANI
[2024-01-25 20:24:44,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e601b1-7d82-4631-9e2f-014fe3809ed1/GCF_024159085.1_ASM2415908v1_genomic.fna.gz --refList GCF_024159085.1_ASM2415908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024159085.1_ASM2415908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:49,987] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:49,994] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:24:49,994] [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_000008465.1	s__Idiomarina loihiensis	93.3571	830	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_003987255.1	s__Idiomarina ramblicola	84.4967	657	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116625.1	s__Idiomarina abyssalis	84.153	636	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
GCF_900100855.1	s__Idiomarina zobellii	80.2122	379	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_003987095.1	s__Idiomarina piscisalsi	80.1832	356	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	79.8869	376	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_002808045.1	s__Idiomarina sp002808045	79.477	395	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_003987185.1	s__Idiomarina aquatica	78.6963	211	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
GCF_003999375.1	s__Pseudidiomarina mangrovi	77.3896	82	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:49,996] [INFO] GTDB search result was written to GCF_024159085.1_ASM2415908v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:49,996] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:50,002] [INFO] DFAST_QC result json was written to GCF_024159085.1_ASM2415908v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:50,002] [INFO] DFAST_QC completed!
[2024-01-25 20:24:50,002] [INFO] Total running time: 0h0m44s