[2024-01-25 18:54:05,617] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:05,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:05,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4e42090-8abd-497e-8bcc-890a764b70bd/dqc_reference
[2024-01-25 18:54:06,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:06,765] [INFO] Task started: Prodigal
[2024-01-25 18:54:06,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bb08729-fdcd-4b4e-b8ab-91c22eebf8fc/GCF_002238335.1_ASM223833v1_genomic.fna.gz | prodigal -d GCF_002238335.1_ASM223833v1_genomic.fna/cds.fna -a GCF_002238335.1_ASM223833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:09,650] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:09,650] [INFO] Task started: HMMsearch
[2024-01-25 18:54:09,650] [INFO] Running command: hmmsearch --tblout GCF_002238335.1_ASM223833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4e42090-8abd-497e-8bcc-890a764b70bd/dqc_reference/reference_markers.hmm GCF_002238335.1_ASM223833v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:09,835] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:09,836] [INFO] Found 6/6 markers.
[2024-01-25 18:54:09,858] [INFO] Query marker FASTA was written to GCF_002238335.1_ASM223833v1_genomic.fna/markers.fasta
[2024-01-25 18:54:09,859] [INFO] Task started: Blastn
[2024-01-25 18:54:09,859] [INFO] Running command: blastn -query GCF_002238335.1_ASM223833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4e42090-8abd-497e-8bcc-890a764b70bd/dqc_reference/reference_markers.fasta -out GCF_002238335.1_ASM223833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:10,393] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:10,396] [INFO] Selected 19 target genomes.
[2024-01-25 18:54:10,397] [INFO] Target genome list was writen to GCF_002238335.1_ASM223833v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:10,411] [INFO] Task started: fastANI
[2024-01-25 18:54:10,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb08729-fdcd-4b4e-b8ab-91c22eebf8fc/GCF_002238335.1_ASM223833v1_genomic.fna.gz --refList GCF_002238335.1_ASM223833v1_genomic.fna/target_genomes.txt --output GCF_002238335.1_ASM223833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:15,224] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:15,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4e42090-8abd-497e-8bcc-890a764b70bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:15,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4e42090-8abd-497e-8bcc-890a764b70bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:15,237] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:54:15,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:15,237] [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
Campylobacter avium	strain=LMG 24591	GCA_002238335.1	522485	522485	type	True	100.0	578	579	95	conclusive
Campylobacter lari subsp. concheus	strain=LMG 21009	GCA_008245025.1	488545	201	type	True	77.6619	97	579	95	below_threshold
Campylobacter peloridis	strain=LMG 23910	GCA_000816785.1	488546	488546	type	True	77.5022	93	579	95	below_threshold
Campylobacter lari	strain=NCTC11352	GCA_900446615.1	201	201	type	True	77.4823	108	579	95	below_threshold
Campylobacter lari subsp. lari	strain=LMG 8846	GCA_013372185.1	650054	201	type	True	77.4297	107	579	95	below_threshold
Campylobacter helveticus	strain=NCTC12470	GCA_900446405.1	28898	28898	type	True	77.4162	123	579	95	below_threshold
Campylobacter lari	strain=FDAARGOS_1101	GCA_016726265.1	201	201	type	True	77.3921	109	579	95	below_threshold
Campylobacter helveticus	strain=ATCC 51209	GCA_002080395.1	28898	28898	type	True	77.3917	124	579	95	below_threshold
Campylobacter armoricus	strain=CCUG 73571	GCA_013372105.1	2505970	2505970	type	True	77.2916	102	579	95	below_threshold
Campylobacter ornithocola	strain=LMG 29815	GCA_013201605.1	1848766	1848766	type	True	77.2231	100	579	95	below_threshold
Campylobacter lari subsp. concheus	strain=CCUG 55786	GCA_008802005.1	488545	201	type	True	77.1744	94	579	95	below_threshold
Campylobacter volucris	strain=LMG 24380	GCA_008245045.1	1031542	1031542	type	True	77.1665	107	579	95	below_threshold
Campylobacter aviculae	strain=MIT17-670	GCA_005406215.1	2510190	2510190	type	True	77.1252	79	579	95	below_threshold
Campylobacter vulpis	strain=251/13	GCA_002738305.1	1655500	1655500	type	True	77.0379	108	579	95	below_threshold
Campylobacter volucris	strain=CCUG 57498	GCA_008801985.1	1031542	1031542	type	True	76.9103	106	579	95	below_threshold
Campylobacter helveticus	strain=ATCC 51209	GCA_900176295.1	28898	28898	type	True	76.8039	123	579	95	below_threshold
Campylobacter lari subsp. lari	strain=ATCC 35221	GCA_900111465.1	650054	201	type	True	76.7233	101	579	95	below_threshold
Campylobacter ornithocola	strain=WBE38	GCA_001705345.1	1848766	1848766	type	True	76.6166	96	579	95	below_threshold
Campylobacter armoricus	strain=CA656	GCA_006176165.1	2505970	2505970	type	True	76.6101	98	579	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:15,239] [INFO] DFAST Taxonomy check result was written to GCF_002238335.1_ASM223833v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:15,239] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:15,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:15,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4e42090-8abd-497e-8bcc-890a764b70bd/dqc_reference/checkm_data
[2024-01-25 18:54:15,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:15,260] [INFO] Task started: CheckM
[2024-01-25 18:54:15,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002238335.1_ASM223833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002238335.1_ASM223833v1_genomic.fna/checkm_input GCF_002238335.1_ASM223833v1_genomic.fna/checkm_result
[2024-01-25 18:54:30,227] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:30,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:30,244] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:30,244] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:30,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002238335.1_ASM223833v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:30,244] [INFO] Task started: Blastn
[2024-01-25 18:54:30,244] [INFO] Running command: blastn -query GCF_002238335.1_ASM223833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4e42090-8abd-497e-8bcc-890a764b70bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_002238335.1_ASM223833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:31,007] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:31,009] [INFO] Selected 21 target genomes.
[2024-01-25 18:54:31,010] [INFO] Target genome list was writen to GCF_002238335.1_ASM223833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:31,024] [INFO] Task started: fastANI
[2024-01-25 18:54:31,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb08729-fdcd-4b4e-b8ab-91c22eebf8fc/GCF_002238335.1_ASM223833v1_genomic.fna.gz --refList GCF_002238335.1_ASM223833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002238335.1_ASM223833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:38,130] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:38,142] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:38,142] [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_002238335.1	s__Campylobacter_D avium	100.0	579	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.95	99.95	0.99	0.99	2	conclusive
GCF_000816785.1	s__Campylobacter_D peloridis	77.7389	95	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.24	96.49	0.94	0.89	3	-
GCF_006864365.1	s__Campylobacter_D sp006864365	77.6863	144	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008245025.1	s__Campylobacter_D concheus	77.6619	97	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.27	98.88	0.96	0.94	4	-
GCF_000816305.1	s__Campylobacter_D subantarcticus	77.6486	80	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.30	98.60	0.97	0.94	3	-
GCF_013372185.1	s__Campylobacter_D lari	77.5514	109	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.73	98.09	0.96	0.93	13	-
GCF_006864535.1	s__Campylobacter_D sp006864535	77.4941	160	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.50	97.50	0.96	0.93	3	-
GCF_002080395.1	s__Campylobacter_D helveticus	77.3917	124	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.44	98.95	0.97	0.95	14	-
GCF_013372105.1	s__Campylobacter_D armoricus	77.2025	101	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.30	98.87	0.93	0.88	11	-
GCF_013201605.1	s__Campylobacter_D ornithocola	77.2001	98	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.99	99.99	0.98	0.98	2	-
GCF_016599045.1	s__Campylobacter_D sp016599045	77.134	85	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.00	98.98	0.95	0.93	3	-
GCF_008011665.1	s__Campylobacter_D volucris_A	77.0863	94	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006864455.1	s__Campylobacter_D sp006864455	77.0795	144	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002179165.1	s__Campylobacter_D jejuni_B	77.0644	97	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002738305.1	s__Campylobacter_D vulpis	77.0379	108	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.20	98.60	0.92	0.87	15	-
GCF_008245045.1	s__Campylobacter_D volucris	76.9643	108	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	98.63	97.46	0.95	0.86	15	-
GCF_004357905.1	s__Campylobacter_D lari_D	76.9256	98	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005406205.1	s__Campylobacter_D estrildidarum	76.7706	84	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009362725.1	s__Campylobacter_D hepaticus_A	76.6493	103	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004378855.1	s__Campylobacter_D sp004378855	76.6395	123	579	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:38,144] [INFO] GTDB search result was written to GCF_002238335.1_ASM223833v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:38,145] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:38,149] [INFO] DFAST_QC result json was written to GCF_002238335.1_ASM223833v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:38,149] [INFO] DFAST_QC completed!
[2024-01-25 18:54:38,149] [INFO] Total running time: 0h0m33s