[2023-06-19 08:50:18,772] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:50:18,776] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:50:18,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgc70f4573-915d-4488-a8fc-9665f4c302a1/dqc_reference
[2023-06-19 08:50:19,984] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:50:20,005] [INFO] Task started: Prodigal
[2023-06-19 08:50:20,006] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8866919-eaff-4ed0-aea6-6a7ae4d4741c/GCA_018065885.1_ASM1806588v1_genomic.fna.gz | prodigal -d GCA_018065885.1_ASM1806588v1_genomic.fna/cds.fna -a GCA_018065885.1_ASM1806588v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:50:34,635] [INFO] Task succeeded: Prodigal
[2023-06-19 08:50:34,636] [INFO] Task started: HMMsearch
[2023-06-19 08:50:34,636] [INFO] Running command: hmmsearch --tblout GCA_018065885.1_ASM1806588v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc70f4573-915d-4488-a8fc-9665f4c302a1/dqc_reference/reference_markers.hmm GCA_018065885.1_ASM1806588v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:50:34,880] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:50:34,881] [INFO] Found 6/6 markers.
[2023-06-19 08:50:34,913] [INFO] Query marker FASTA was written to GCA_018065885.1_ASM1806588v1_genomic.fna/markers.fasta
[2023-06-19 08:50:34,913] [INFO] Task started: Blastn
[2023-06-19 08:50:34,914] [INFO] Running command: blastn -query GCA_018065885.1_ASM1806588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc70f4573-915d-4488-a8fc-9665f4c302a1/dqc_reference/reference_markers.fasta -out GCA_018065885.1_ASM1806588v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:50:35,570] [INFO] Task succeeded: Blastn
[2023-06-19 08:50:35,575] [INFO] Selected 32 target genomes.
[2023-06-19 08:50:35,576] [INFO] Target genome list was writen to GCA_018065885.1_ASM1806588v1_genomic.fna/target_genomes.txt
[2023-06-19 08:50:35,582] [INFO] Task started: fastANI
[2023-06-19 08:50:35,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8866919-eaff-4ed0-aea6-6a7ae4d4741c/GCA_018065885.1_ASM1806588v1_genomic.fna.gz --refList GCA_018065885.1_ASM1806588v1_genomic.fna/target_genomes.txt --output GCA_018065885.1_ASM1806588v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:51:00,400] [INFO] Task succeeded: fastANI
[2023-06-19 08:51:00,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc70f4573-915d-4488-a8fc-9665f4c302a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:51:00,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc70f4573-915d-4488-a8fc-9665f4c302a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:51:00,402] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:51:00,402] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:51:00,403] [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
--------------------------------------------------------------------------------
[2023-06-19 08:51:00,406] [INFO] DFAST Taxonomy check result was written to GCA_018065885.1_ASM1806588v1_genomic.fna/tc_result.tsv
[2023-06-19 08:51:00,407] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:51:00,407] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:51:00,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc70f4573-915d-4488-a8fc-9665f4c302a1/dqc_reference/checkm_data
[2023-06-19 08:51:00,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:51:00,442] [INFO] Task started: CheckM
[2023-06-19 08:51:00,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018065885.1_ASM1806588v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018065885.1_ASM1806588v1_genomic.fna/checkm_input GCA_018065885.1_ASM1806588v1_genomic.fna/checkm_result
[2023-06-19 08:51:46,410] [INFO] Task succeeded: CheckM
[2023-06-19 08:51:46,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:51:46,438] [INFO] ===== Completeness check finished =====
[2023-06-19 08:51:46,438] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:51:46,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018065885.1_ASM1806588v1_genomic.fna/markers.fasta)
[2023-06-19 08:51:46,439] [INFO] Task started: Blastn
[2023-06-19 08:51:46,439] [INFO] Running command: blastn -query GCA_018065885.1_ASM1806588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc70f4573-915d-4488-a8fc-9665f4c302a1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018065885.1_ASM1806588v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:51:47,436] [INFO] Task succeeded: Blastn
[2023-06-19 08:51:47,443] [INFO] Selected 27 target genomes.
[2023-06-19 08:51:47,443] [INFO] Target genome list was writen to GCA_018065885.1_ASM1806588v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:51:47,482] [INFO] Task started: fastANI
[2023-06-19 08:51:47,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8866919-eaff-4ed0-aea6-6a7ae4d4741c/GCA_018065885.1_ASM1806588v1_genomic.fna.gz --refList GCA_018065885.1_ASM1806588v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018065885.1_ASM1806588v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:52:00,283] [INFO] Task succeeded: fastANI
[2023-06-19 08:52:00,306] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:52:00,306] [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
GCA_018065885.1	s__Limimorpha sp018065885	100.0	662	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017477425.1	s__Limimorpha sp017477425	78.3016	168	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786745.1	s__Limimorpha sp902786745	78.2108	160	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.85	95.75	0.88	0.85	4	-
GCA_001543395.1	s__Limimorpha sp001543395	78.2048	107	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	99.91	99.91	0.93	0.93	2	-
GCA_017460915.1	s__Limimorpha sp017460915	78.1001	155	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785755.1	s__Limimorpha sp902785755	78.0638	188	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.44	95.41	0.82	0.81	3	-
GCA_017395365.1	s__Limimorpha sp017395365	78.0109	102	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317155.1	s__Limimorpha sp900317155	77.9816	169	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.66	95.75	0.85	0.80	7	-
GCA_017645245.1	s__Limimorpha sp017645245	77.9517	111	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017539045.1	s__Limimorpha sp017539045	77.9463	122	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317055.1	s__Limimorpha sp900317055	77.9384	146	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017549805.1	s__Limimorpha sp017549805	77.8643	122	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802535.1	s__Limimorpha sp902802535	77.7025	169	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.04	96.04	0.77	0.77	2	-
GCA_016291135.1	s__Limimorpha sp016291135	77.6399	99	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769815.1	s__Limimorpha sp902769815	77.5868	148	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902770835.1	s__Limimorpha sp902770835	77.5782	195	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.42	95.03	0.80	0.78	4	-
GCA_905234765.1	s__Limimorpha sp905234765	77.5709	150	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318465.1	s__Limimorpha sp900318465	77.4878	164	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	97.54	95.09	0.89	0.78	3	-
GCA_002396205.1	s__Limimorpha sp002396205	77.4706	167	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769875.1	s__Limimorpha sp902769875	77.4678	164	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017439405.1	s__Limimorpha sp017439405	77.4247	160	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233685.1	s__Limimorpha sp905233685	77.3731	166	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789915.1	s__Limimorpha sp902789915	77.3377	135	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.09	95.09	0.73	0.73	2	-
GCA_902771635.1	s__Limimorpha sp902771635	77.2041	127	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428285.1	s__Limimorpha sp017428285	77.1554	130	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017508895.1	s__Limimorpha sp017508895	77.0927	141	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234455.1	s__Limimorpha sp905234455	77.0513	95	674	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:52:00,309] [INFO] GTDB search result was written to GCA_018065885.1_ASM1806588v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:52:00,309] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:52:00,320] [INFO] DFAST_QC result json was written to GCA_018065885.1_ASM1806588v1_genomic.fna/dqc_result.json
[2023-06-19 08:52:00,320] [INFO] DFAST_QC completed!
[2023-06-19 08:52:00,320] [INFO] Total running time: 0h1m42s