[2024-01-24 13:31:35,424] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg02e0acdf-5025-491c-9b1e-a23d6aaa8288/dqc_reference
[2024-01-24 13:31:36,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,890] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg01449d27-62e2-490a-a621-bb8db4bc4ad3/GCF_004122035.1_ASM412203v1_genomic.fna.gz | prodigal -d GCF_004122035.1_ASM412203v1_genomic.fna/cds.fna -a GCF_004122035.1_ASM412203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:54,318] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:54,318] [INFO] Task started: HMMsearch
[2024-01-24 13:31:54,318] [INFO] Running command: hmmsearch --tblout GCF_004122035.1_ASM412203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02e0acdf-5025-491c-9b1e-a23d6aaa8288/dqc_reference/reference_markers.hmm GCF_004122035.1_ASM412203v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:54,628] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:54,630] [INFO] Found 6/6 markers.
[2024-01-24 13:31:54,677] [INFO] Query marker FASTA was written to GCF_004122035.1_ASM412203v1_genomic.fna/markers.fasta
[2024-01-24 13:31:54,678] [INFO] Task started: Blastn
[2024-01-24 13:31:54,678] [INFO] Running command: blastn -query GCF_004122035.1_ASM412203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e0acdf-5025-491c-9b1e-a23d6aaa8288/dqc_reference/reference_markers.fasta -out GCF_004122035.1_ASM412203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:55,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:55,337] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:55,338] [INFO] Target genome list was writen to GCF_004122035.1_ASM412203v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:55,359] [INFO] Task started: fastANI
[2024-01-24 13:31:55,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg01449d27-62e2-490a-a621-bb8db4bc4ad3/GCF_004122035.1_ASM412203v1_genomic.fna.gz --refList GCF_004122035.1_ASM412203v1_genomic.fna/target_genomes.txt --output GCF_004122035.1_ASM412203v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:09,920] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:09,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02e0acdf-5025-491c-9b1e-a23d6aaa8288/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:09,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02e0acdf-5025-491c-9b1e-a23d6aaa8288/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:09,931] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:09,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:09,932] [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
Ancylomarina salipaludis	strain=SHSM-M15	GCA_004122035.1	2501299	2501299	type	True	100.0	1355	1358	95	conclusive
Ancylomarina subtilis	strain=DSM 28825	GCA_004217115.1	1639035	1639035	type	True	88.3882	1127	1358	95	below_threshold
Labilibaculum filiforme	strain=59.16B	GCA_002843315.1	1940526	1940526	type	True	78.0531	194	1358	95	below_threshold
Marinifilum breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	78.0104	240	1358	95	below_threshold
Marinifilum caeruleilacunae	strain=JC070	GCA_013141825.1	2499076	2499076	type	True	77.9292	231	1358	95	below_threshold
Labilibaculum manganireducens	strain=59.10-2M	GCA_002843385.1	1940525	1940525	type	True	77.8837	212	1358	95	below_threshold
Labilibaculum antarcticum	strain=SPP2	GCA_002356295.1	1717717	1717717	type	True	77.8396	233	1358	95	below_threshold
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	77.8032	248	1358	95	below_threshold
Ancylomarina longa	strain=T3-2 S1-C	GCA_003996985.1	2487017	2487017	type	True	77.6581	167	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:09,934] [INFO] DFAST Taxonomy check result was written to GCF_004122035.1_ASM412203v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:09,935] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:09,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:09,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02e0acdf-5025-491c-9b1e-a23d6aaa8288/dqc_reference/checkm_data
[2024-01-24 13:32:09,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:09,992] [INFO] Task started: CheckM
[2024-01-24 13:32:09,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004122035.1_ASM412203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004122035.1_ASM412203v1_genomic.fna/checkm_input GCF_004122035.1_ASM412203v1_genomic.fna/checkm_result
[2024-01-24 13:33:02,906] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:02,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,931] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:02,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:02,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004122035.1_ASM412203v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:02,933] [INFO] Task started: Blastn
[2024-01-24 13:33:02,933] [INFO] Running command: blastn -query GCF_004122035.1_ASM412203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02e0acdf-5025-491c-9b1e-a23d6aaa8288/dqc_reference/reference_markers_gtdb.fasta -out GCF_004122035.1_ASM412203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:03,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:03,881] [INFO] Selected 7 target genomes.
[2024-01-24 13:33:03,881] [INFO] Target genome list was writen to GCF_004122035.1_ASM412203v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:03,887] [INFO] Task started: fastANI
[2024-01-24 13:33:03,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg01449d27-62e2-490a-a621-bb8db4bc4ad3/GCF_004122035.1_ASM412203v1_genomic.fna.gz --refList GCF_004122035.1_ASM412203v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004122035.1_ASM412203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:11,514] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:11,528] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:11,528] [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_004122035.1	s__Ancylomarina salipaludis	100.0	1355	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004217115.1	s__Ancylomarina subtilis	88.3881	1127	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863355.1	s__Ancylomarina euxinus	81.7212	890	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016744515.1	s__Ancylomarina sp016744515	80.5998	584	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009669305.1	s__Ancylomarina sp009669305	80.0671	556	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141825.1	s__Marinifilum sp013141825	77.9446	230	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003996985.1	s__Ancylomarina_A longa	77.6673	168	1358	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,538] [INFO] GTDB search result was written to GCF_004122035.1_ASM412203v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:11,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:11,542] [INFO] DFAST_QC result json was written to GCF_004122035.1_ASM412203v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:11,542] [INFO] DFAST_QC completed!
[2024-01-24 13:33:11,542] [INFO] Total running time: 0h1m36s