[2024-01-25 18:07:51,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:51,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:51,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg734273a6-5fa0-422a-a944-ffa02e62ef4e/dqc_reference
[2024-01-25 18:07:52,648] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:52,649] [INFO] Task started: Prodigal
[2024-01-25 18:07:52,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg61cfe323-0925-47db-9f59-9e04c8b6eada/GCF_003581615.1_ASM358161v1_genomic.fna.gz | prodigal -d GCF_003581615.1_ASM358161v1_genomic.fna/cds.fna -a GCF_003581615.1_ASM358161v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:09,031] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:09,031] [INFO] Task started: HMMsearch
[2024-01-25 18:08:09,031] [INFO] Running command: hmmsearch --tblout GCF_003581615.1_ASM358161v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg734273a6-5fa0-422a-a944-ffa02e62ef4e/dqc_reference/reference_markers.hmm GCF_003581615.1_ASM358161v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:09,256] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:09,257] [INFO] Found 6/6 markers.
[2024-01-25 18:08:09,287] [INFO] Query marker FASTA was written to GCF_003581615.1_ASM358161v1_genomic.fna/markers.fasta
[2024-01-25 18:08:09,288] [INFO] Task started: Blastn
[2024-01-25 18:08:09,288] [INFO] Running command: blastn -query GCF_003581615.1_ASM358161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg734273a6-5fa0-422a-a944-ffa02e62ef4e/dqc_reference/reference_markers.fasta -out GCF_003581615.1_ASM358161v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:09,932] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:09,935] [INFO] Selected 14 target genomes.
[2024-01-25 18:08:09,936] [INFO] Target genome list was writen to GCF_003581615.1_ASM358161v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:09,970] [INFO] Task started: fastANI
[2024-01-25 18:08:09,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg61cfe323-0925-47db-9f59-9e04c8b6eada/GCF_003581615.1_ASM358161v1_genomic.fna.gz --refList GCF_003581615.1_ASM358161v1_genomic.fna/target_genomes.txt --output GCF_003581615.1_ASM358161v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:21,105] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:21,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg734273a6-5fa0-422a-a944-ffa02e62ef4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:21,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg734273a6-5fa0-422a-a944-ffa02e62ef4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:21,115] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:21,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:21,115] [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
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	100.0	1222	1224	95	conclusive
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	83.4535	797	1224	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	82.5657	876	1224	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	82.0414	782	1224	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	81.9685	728	1224	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	81.9566	742	1224	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	81.5545	740	1224	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	81.1492	701	1224	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	81.1248	706	1224	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	79.6973	624	1224	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	79.6959	629	1224	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	78.4945	439	1224	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	78.411	432	1224	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.2346	206	1224	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:21,117] [INFO] DFAST Taxonomy check result was written to GCF_003581615.1_ASM358161v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:21,117] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:21,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:21,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg734273a6-5fa0-422a-a944-ffa02e62ef4e/dqc_reference/checkm_data
[2024-01-25 18:08:21,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:21,156] [INFO] Task started: CheckM
[2024-01-25 18:08:21,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003581615.1_ASM358161v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003581615.1_ASM358161v1_genomic.fna/checkm_input GCF_003581615.1_ASM358161v1_genomic.fna/checkm_result
[2024-01-25 18:09:08,121] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:08,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:08,150] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:08,150] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:08,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003581615.1_ASM358161v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:08,151] [INFO] Task started: Blastn
[2024-01-25 18:09:08,151] [INFO] Running command: blastn -query GCF_003581615.1_ASM358161v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg734273a6-5fa0-422a-a944-ffa02e62ef4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003581615.1_ASM358161v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:09,013] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:09,016] [INFO] Selected 9 target genomes.
[2024-01-25 18:09:09,016] [INFO] Target genome list was writen to GCF_003581615.1_ASM358161v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:09,031] [INFO] Task started: fastANI
[2024-01-25 18:09:09,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg61cfe323-0925-47db-9f59-9e04c8b6eada/GCF_003581615.1_ASM358161v1_genomic.fna.gz --refList GCF_003581615.1_ASM358161v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003581615.1_ASM358161v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:17,375] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:17,382] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:17,382] [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_003581615.1	s__Muricauda lutimaris	100.0	1222	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002167435.2	s__Muricauda sp002167435	89.1242	920	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	89.0284	950	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	83.4648	796	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	83.076	799	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	82.9148	830	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	82.6539	787	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	82.0414	782	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCA_002699205.1	s__Muricauda sp002699205	81.877	713	1224	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:17,384] [INFO] GTDB search result was written to GCF_003581615.1_ASM358161v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:17,384] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:17,387] [INFO] DFAST_QC result json was written to GCF_003581615.1_ASM358161v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:17,387] [INFO] DFAST_QC completed!
[2024-01-25 18:09:17,387] [INFO] Total running time: 0h1m26s