[2024-01-25 20:02:20,590] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:20,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:20,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg50b24e9e-214b-48e5-866b-d688b1f691eb/dqc_reference
[2024-01-25 20:02:21,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:21,753] [INFO] Task started: Prodigal
[2024-01-25 20:02:21,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fd9d60f-ddc9-418c-9f38-9b38d2b2edf5/GCF_001310955.1_ASM131095v1_genomic.fna.gz | prodigal -d GCF_001310955.1_ASM131095v1_genomic.fna/cds.fna -a GCF_001310955.1_ASM131095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:38,335] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:38,335] [INFO] Task started: HMMsearch
[2024-01-25 20:02:38,335] [INFO] Running command: hmmsearch --tblout GCF_001310955.1_ASM131095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50b24e9e-214b-48e5-866b-d688b1f691eb/dqc_reference/reference_markers.hmm GCF_001310955.1_ASM131095v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:38,613] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:38,614] [INFO] Found 6/6 markers.
[2024-01-25 20:02:38,657] [INFO] Query marker FASTA was written to GCF_001310955.1_ASM131095v1_genomic.fna/markers.fasta
[2024-01-25 20:02:38,657] [INFO] Task started: Blastn
[2024-01-25 20:02:38,657] [INFO] Running command: blastn -query GCF_001310955.1_ASM131095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b24e9e-214b-48e5-866b-d688b1f691eb/dqc_reference/reference_markers.fasta -out GCF_001310955.1_ASM131095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:39,251] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:39,258] [INFO] Selected 13 target genomes.
[2024-01-25 20:02:39,259] [INFO] Target genome list was writen to GCF_001310955.1_ASM131095v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:39,267] [INFO] Task started: fastANI
[2024-01-25 20:02:39,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd9d60f-ddc9-418c-9f38-9b38d2b2edf5/GCF_001310955.1_ASM131095v1_genomic.fna.gz --refList GCF_001310955.1_ASM131095v1_genomic.fna/target_genomes.txt --output GCF_001310955.1_ASM131095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:52,471] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:52,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50b24e9e-214b-48e5-866b-d688b1f691eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:52,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50b24e9e-214b-48e5-866b-d688b1f691eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:52,478] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:52,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:52,478] [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
Marinifilum fragile	strain=JCM 15579	GCA_001310955.1	570161	570161	type	True	100.0	1527	1534	95	conclusive
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	89.1825	1295	1534	95	below_threshold
Marinifilum breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	88.0722	1264	1534	95	below_threshold
Marinifilum caeruleilacunae	strain=JC070	GCA_013141825.1	2499076	2499076	type	True	82.3312	940	1534	95	below_threshold
Labilibaculum manganireducens	strain=59.10-2M	GCA_002843385.1	1940525	1940525	type	True	77.9772	403	1534	95	below_threshold
Labilibaculum filiforme	strain=59.16B	GCA_002843315.1	1940526	1940526	type	True	77.8245	388	1534	95	below_threshold
Labilibaculum antarcticum	strain=SPP2	GCA_002356295.1	1717717	1717717	type	True	77.7591	402	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:52,479] [INFO] DFAST Taxonomy check result was written to GCF_001310955.1_ASM131095v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:52,480] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:52,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:52,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50b24e9e-214b-48e5-866b-d688b1f691eb/dqc_reference/checkm_data
[2024-01-25 20:02:52,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:52,527] [INFO] Task started: CheckM
[2024-01-25 20:02:52,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001310955.1_ASM131095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001310955.1_ASM131095v1_genomic.fna/checkm_input GCF_001310955.1_ASM131095v1_genomic.fna/checkm_result
[2024-01-25 20:03:40,068] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:40,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:40,084] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:40,084] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:40,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001310955.1_ASM131095v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:40,086] [INFO] Task started: Blastn
[2024-01-25 20:03:40,086] [INFO] Running command: blastn -query GCF_001310955.1_ASM131095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b24e9e-214b-48e5-866b-d688b1f691eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_001310955.1_ASM131095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:40,929] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:40,932] [INFO] Selected 9 target genomes.
[2024-01-25 20:03:40,932] [INFO] Target genome list was writen to GCF_001310955.1_ASM131095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:40,942] [INFO] Task started: fastANI
[2024-01-25 20:03:40,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd9d60f-ddc9-418c-9f38-9b38d2b2edf5/GCF_001310955.1_ASM131095v1_genomic.fna.gz --refList GCF_001310955.1_ASM131095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001310955.1_ASM131095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:51,207] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:51,215] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:51,216] [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_001310955.1	s__Marinifilum fragile	100.0	1527	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003610555.1	s__Marinifilum flexuosum	89.1825	1295	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202155.1	s__Marinifilum breve	88.0702	1264	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141825.1	s__Marinifilum sp013141825	82.3394	939	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295825.1	s__Marinifilum sp009295825	79.488	743	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342745.1	s__Labilibaculum sp016342745	78.3686	467	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843315.1	s__Labilibaculum filiforme	77.8074	390	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863355.1	s__Ancylomarina euxinus	77.586	234	1534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:51,217] [INFO] GTDB search result was written to GCF_001310955.1_ASM131095v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:51,219] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:51,221] [INFO] DFAST_QC result json was written to GCF_001310955.1_ASM131095v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:51,221] [INFO] DFAST_QC completed!
[2024-01-25 20:03:51,221] [INFO] Total running time: 0h1m31s