[2024-01-24 14:39:15,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg2494aee8-b134-4ecc-b2a9-70cbd34b0070/dqc_reference
[2024-01-24 14:39:16,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,482] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,483] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6de6330-689b-4cef-bc15-85e256b3082c/GCF_014639155.1_ASM1463915v1_genomic.fna.gz | prodigal -d GCF_014639155.1_ASM1463915v1_genomic.fna/cds.fna -a GCF_014639155.1_ASM1463915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:30,347] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:30,348] [INFO] Task started: HMMsearch
[2024-01-24 14:39:30,348] [INFO] Running command: hmmsearch --tblout GCF_014639155.1_ASM1463915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2494aee8-b134-4ecc-b2a9-70cbd34b0070/dqc_reference/reference_markers.hmm GCF_014639155.1_ASM1463915v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:30,710] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:30,711] [INFO] Found 6/6 markers.
[2024-01-24 14:39:30,760] [INFO] Query marker FASTA was written to GCF_014639155.1_ASM1463915v1_genomic.fna/markers.fasta
[2024-01-24 14:39:30,761] [INFO] Task started: Blastn
[2024-01-24 14:39:30,761] [INFO] Running command: blastn -query GCF_014639155.1_ASM1463915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2494aee8-b134-4ecc-b2a9-70cbd34b0070/dqc_reference/reference_markers.fasta -out GCF_014639155.1_ASM1463915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:31,390] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:31,393] [INFO] Selected 26 target genomes.
[2024-01-24 14:39:31,394] [INFO] Target genome list was writen to GCF_014639155.1_ASM1463915v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:31,403] [INFO] Task started: fastANI
[2024-01-24 14:39:31,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6de6330-689b-4cef-bc15-85e256b3082c/GCF_014639155.1_ASM1463915v1_genomic.fna.gz --refList GCF_014639155.1_ASM1463915v1_genomic.fna/target_genomes.txt --output GCF_014639155.1_ASM1463915v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:55,852] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:55,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2494aee8-b134-4ecc-b2a9-70cbd34b0070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:55,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2494aee8-b134-4ecc-b2a9-70cbd34b0070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:55,866] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:55,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:55,867] [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
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	100.0	1825	1825	95	conclusive
Paenibacillus anaericanus	strain=DSM 15890	GCA_003994475.1	170367	170367	type	True	82.4184	1139	1825	95	below_threshold
Paenibacillus lutimineralis	strain=MBLB1234	GCA_003991425.1	2707005	2707005	type	True	78.6199	318	1825	95	below_threshold
Fontibacillus panacisegetis	strain=DSM 28129	GCA_900102215.1	670482	670482	type	True	78.1749	301	1825	95	below_threshold
Fontibacillus solani	strain=CECT 8693	GCA_014138385.1	1572857	1572857	type	True	78.1086	303	1825	95	below_threshold
Paenibacillus lentus	strain=DSM 25539	GCA_003931855.1	1338368	1338368	type	True	77.9795	238	1825	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.8563	228	1825	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.8502	257	1825	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	77.836	250	1825	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	77.8356	260	1825	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	77.8198	262	1825	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.5867	148	1825	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.5831	85	1825	95	below_threshold
Paenibacillus lemnae	strain=L7-75	GCA_012933385.1	1330551	1330551	type	True	77.5281	79	1825	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	77.2024	168	1825	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	77.1739	81	1825	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.0941	81	1825	95	below_threshold
Paenibacillus kobensis	strain=NBRC 15729	GCA_004000825.1	59841	59841	type	True	76.8398	50	1825	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:55,868] [INFO] DFAST Taxonomy check result was written to GCF_014639155.1_ASM1463915v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:55,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:55,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:55,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2494aee8-b134-4ecc-b2a9-70cbd34b0070/dqc_reference/checkm_data
[2024-01-24 14:39:55,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:55,923] [INFO] Task started: CheckM
[2024-01-24 14:39:55,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639155.1_ASM1463915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639155.1_ASM1463915v1_genomic.fna/checkm_input GCF_014639155.1_ASM1463915v1_genomic.fna/checkm_result
[2024-01-24 14:40:36,527] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:36,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:36,545] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:36,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:36,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639155.1_ASM1463915v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:36,545] [INFO] Task started: Blastn
[2024-01-24 14:40:36,546] [INFO] Running command: blastn -query GCF_014639155.1_ASM1463915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2494aee8-b134-4ecc-b2a9-70cbd34b0070/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639155.1_ASM1463915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:37,349] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:37,353] [INFO] Selected 20 target genomes.
[2024-01-24 14:40:37,353] [INFO] Target genome list was writen to GCF_014639155.1_ASM1463915v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:37,366] [INFO] Task started: fastANI
[2024-01-24 14:40:37,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6de6330-689b-4cef-bc15-85e256b3082c/GCF_014639155.1_ASM1463915v1_genomic.fna.gz --refList GCF_014639155.1_ASM1463915v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639155.1_ASM1463915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:56,189] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:56,204] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:56,204] [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_014639155.1	s__Paenibacillus_A segetis	100.0	1825	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003994475.1	s__Paenibacillus_A anaericanus	82.4163	1139	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991425.1	s__Paenibacillus_A lutimineralis	78.6199	318	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337355.1	s__Paenibacillus_A phaseoli	78.4093	303	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102215.1	s__Paenibacillus_A panacisegetis	78.1868	300	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.17	97.17	0.85	0.85	2	-
GCF_018403325.1	s__Paenibacillus_A vini	78.1806	314	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.00	98.00	0.91	0.91	2	-
GCF_001403875.1	s__Paenibacillus_A ihumii	77.8789	227	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003614185.1	s__Paenibacillus_A aceti	77.8733	257	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	77.8528	248	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381905.1	s__Paenibacillus_A fonticola	77.827	260	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	77.8154	218	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900069005.2	s__Paenibacillus_A sp900069005	77.7125	239	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.72	99.44	0.97	0.94	3	-
GCF_013359935.1	s__Paenibacillus xylanilyticus	77.605	124	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933385.1	s__Paenibacillus lemnae	77.5518	77	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863965.1	s__Paenibacillus_A oralis	77.5183	227	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908135.1	s__Paenibacillus_Z mendelii	77.2006	80	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374185.1	s__Paenibacillus sp000374185	76.9711	133	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000825.1	s__Paenibacillus_T kobensis	76.8355	50	1825	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:56,206] [INFO] GTDB search result was written to GCF_014639155.1_ASM1463915v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:56,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:56,211] [INFO] DFAST_QC result json was written to GCF_014639155.1_ASM1463915v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:56,211] [INFO] DFAST_QC completed!
[2024-01-24 14:40:56,211] [INFO] Total running time: 0h1m41s