[2023-06-30 07:02:10,044] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:02:10,047] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:02:10,047] [INFO] DQC Reference Directory: /var/lib/cwl/stgad105ce0-b104-4ef5-b73b-4d1e7f4cbb71/dqc_reference
[2023-06-30 07:02:11,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:02:11,582] [INFO] Task started: Prodigal
[2023-06-30 07:02:11,582] [INFO] Running command: gunzip -c /var/lib/cwl/stgefa6efa6-9450-4321-9f36-fb9ed92c9c89/GCA_025210415.1_ASM2521041v1_genomic.fna.gz | prodigal -d GCA_025210415.1_ASM2521041v1_genomic.fna/cds.fna -a GCA_025210415.1_ASM2521041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:02:26,303] [INFO] Task succeeded: Prodigal
[2023-06-30 07:02:26,304] [INFO] Task started: HMMsearch
[2023-06-30 07:02:26,304] [INFO] Running command: hmmsearch --tblout GCA_025210415.1_ASM2521041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad105ce0-b104-4ef5-b73b-4d1e7f4cbb71/dqc_reference/reference_markers.hmm GCA_025210415.1_ASM2521041v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:02:26,566] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:02:26,568] [INFO] Found 6/6 markers.
[2023-06-30 07:02:26,602] [INFO] Query marker FASTA was written to GCA_025210415.1_ASM2521041v1_genomic.fna/markers.fasta
[2023-06-30 07:02:26,602] [INFO] Task started: Blastn
[2023-06-30 07:02:26,602] [INFO] Running command: blastn -query GCA_025210415.1_ASM2521041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad105ce0-b104-4ef5-b73b-4d1e7f4cbb71/dqc_reference/reference_markers.fasta -out GCA_025210415.1_ASM2521041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:02:27,231] [INFO] Task succeeded: Blastn
[2023-06-30 07:02:27,236] [INFO] Selected 9 target genomes.
[2023-06-30 07:02:27,236] [INFO] Target genome list was writen to GCA_025210415.1_ASM2521041v1_genomic.fna/target_genomes.txt
[2023-06-30 07:02:27,238] [INFO] Task started: fastANI
[2023-06-30 07:02:27,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa6efa6-9450-4321-9f36-fb9ed92c9c89/GCA_025210415.1_ASM2521041v1_genomic.fna.gz --refList GCA_025210415.1_ASM2521041v1_genomic.fna/target_genomes.txt --output GCA_025210415.1_ASM2521041v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:02:34,436] [INFO] Task succeeded: fastANI
[2023-06-30 07:02:34,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad105ce0-b104-4ef5-b73b-4d1e7f4cbb71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:02:34,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad105ce0-b104-4ef5-b73b-4d1e7f4cbb71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:02:34,449] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:02:34,450] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:02:34,450] [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 breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	82.7943	692	1133	95	below_threshold
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	82.663	675	1133	95	below_threshold
Marinifilum caeruleilacunae	strain=JC070	GCA_013141825.1	2499076	2499076	type	True	82.4741	618	1133	95	below_threshold
Marinifilum fragile	strain=JCM 15579	GCA_001310955.1	570161	570161	type	True	82.3715	666	1133	95	below_threshold
Ancylomarina longa	strain=T3-2 S1-C	GCA_003996985.1	2487017	2487017	type	True	77.9852	235	1133	95	below_threshold
Ancylomarina subtilis	strain=DSM 28825	GCA_004217115.1	1639035	1639035	type	True	77.8837	157	1133	95	below_threshold
Labilibaculum antarcticum	strain=SPP2	GCA_002356295.1	1717717	1717717	type	True	77.8836	283	1133	95	below_threshold
Labilibaculum filiforme	strain=59.16B	GCA_002843315.1	1940526	1940526	type	True	77.8228	306	1133	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:02:34,452] [INFO] DFAST Taxonomy check result was written to GCA_025210415.1_ASM2521041v1_genomic.fna/tc_result.tsv
[2023-06-30 07:02:34,453] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:02:34,453] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:02:34,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad105ce0-b104-4ef5-b73b-4d1e7f4cbb71/dqc_reference/checkm_data
[2023-06-30 07:02:34,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:02:34,495] [INFO] Task started: CheckM
[2023-06-30 07:02:34,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025210415.1_ASM2521041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025210415.1_ASM2521041v1_genomic.fna/checkm_input GCA_025210415.1_ASM2521041v1_genomic.fna/checkm_result
[2023-06-30 07:03:19,574] [INFO] Task succeeded: CheckM
[2023-06-30 07:03:19,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:03:19,598] [INFO] ===== Completeness check finished =====
[2023-06-30 07:03:19,598] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:03:19,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025210415.1_ASM2521041v1_genomic.fna/markers.fasta)
[2023-06-30 07:03:19,599] [INFO] Task started: Blastn
[2023-06-30 07:03:19,599] [INFO] Running command: blastn -query GCA_025210415.1_ASM2521041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad105ce0-b104-4ef5-b73b-4d1e7f4cbb71/dqc_reference/reference_markers_gtdb.fasta -out GCA_025210415.1_ASM2521041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:03:20,460] [INFO] Task succeeded: Blastn
[2023-06-30 07:03:20,464] [INFO] Selected 7 target genomes.
[2023-06-30 07:03:20,465] [INFO] Target genome list was writen to GCA_025210415.1_ASM2521041v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:03:20,469] [INFO] Task started: fastANI
[2023-06-30 07:03:20,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa6efa6-9450-4321-9f36-fb9ed92c9c89/GCA_025210415.1_ASM2521041v1_genomic.fna.gz --refList GCA_025210415.1_ASM2521041v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025210415.1_ASM2521041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:03:27,308] [INFO] Task succeeded: fastANI
[2023-06-30 07:03:27,319] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 07:03:27,319] [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_003202155.1	s__Marinifilum breve	82.7672	695	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610555.1	s__Marinifilum flexuosum	82.647	676	1133	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	82.4781	618	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310955.1	s__Marinifilum fragile	82.3579	666	1133	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	79.4188	475	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009795715.1	s__Labilibaculum euxinus	78.1417	292	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	97.85	97.85	0.89	0.89	3	-
GCF_002843315.1	s__Labilibaculum filiforme	77.8438	304	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 07:03:27,321] [INFO] GTDB search result was written to GCA_025210415.1_ASM2521041v1_genomic.fna/result_gtdb.tsv
[2023-06-30 07:03:27,322] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:03:27,325] [INFO] DFAST_QC result json was written to GCA_025210415.1_ASM2521041v1_genomic.fna/dqc_result.json
[2023-06-30 07:03:27,325] [INFO] DFAST_QC completed!
[2023-06-30 07:03:27,326] [INFO] Total running time: 0h1m17s