[2024-01-24 11:59:35,604] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg43d9129a-420c-4c5a-858c-7423ad91e1c6/dqc_reference
[2024-01-24 11:59:36,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,814] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f6c87df-9bbb-4309-a704-c67ab6d77011/GCF_019039035.1_ASM1903903v1_genomic.fna.gz | prodigal -d GCF_019039035.1_ASM1903903v1_genomic.fna/cds.fna -a GCF_019039035.1_ASM1903903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:23,971] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:23,972] [INFO] Task started: HMMsearch
[2024-01-24 12:00:23,972] [INFO] Running command: hmmsearch --tblout GCF_019039035.1_ASM1903903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43d9129a-420c-4c5a-858c-7423ad91e1c6/dqc_reference/reference_markers.hmm GCF_019039035.1_ASM1903903v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:24,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:24,443] [INFO] Found 6/6 markers.
[2024-01-24 12:00:24,512] [INFO] Query marker FASTA was written to GCF_019039035.1_ASM1903903v1_genomic.fna/markers.fasta
[2024-01-24 12:00:24,513] [INFO] Task started: Blastn
[2024-01-24 12:00:24,513] [INFO] Running command: blastn -query GCF_019039035.1_ASM1903903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43d9129a-420c-4c5a-858c-7423ad91e1c6/dqc_reference/reference_markers.fasta -out GCF_019039035.1_ASM1903903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:25,237] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:25,243] [INFO] Selected 27 target genomes.
[2024-01-24 12:00:25,243] [INFO] Target genome list was writen to GCF_019039035.1_ASM1903903v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:25,255] [INFO] Task started: fastANI
[2024-01-24 12:00:25,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f6c87df-9bbb-4309-a704-c67ab6d77011/GCF_019039035.1_ASM1903903v1_genomic.fna.gz --refList GCF_019039035.1_ASM1903903v1_genomic.fna/target_genomes.txt --output GCF_019039035.1_ASM1903903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:13,526] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:13,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43d9129a-420c-4c5a-858c-7423ad91e1c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:13,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43d9129a-420c-4c5a-858c-7423ad91e1c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:13,547] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:01:13,547] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:01:13,547] [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
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	82.8341	1498	2957	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.7098	1741	2957	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	82.6707	1580	2957	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	82.6601	1642	2957	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.6516	1685	2957	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	82.6112	1584	2957	95	below_threshold
Corallococcus coralloides	strain=DSM 2259	GCA_000255295.1	184914	184914	type	True	82.5769	1738	2957	95	below_threshold
Corallococcus exiguus	strain=DSM 14696	GCA_009909105.1	83462	83462	type	True	82.4565	1749	2957	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	82.3211	1585	2957	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	82.0535	1829	2957	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	81.9868	1786	2957	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	81.937	1382	2957	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	81.9298	1698	2957	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	81.8225	1742	2957	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	81.8141	1752	2957	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	81.7545	1602	2957	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	81.705	1574	2957	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	81.6603	1718	2957	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	81.5246	1699	2957	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	76.5608	220	2957	95	below_threshold
Jannaschia aquimarina	strain=DSM 28248	GCA_900188045.1	935700	935700	type	True	74.9145	70	2957	95	below_threshold
Jannaschia aquimarina	strain=GSW-M26	GCA_000877395.1	935700	935700	type	True	74.8854	69	2957	95	below_threshold
Actinomadura macra	strain=NBRC 14102	GCA_001552215.1	46164	46164	type	True	74.8561	256	2957	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	74.848	83	2957	95	below_threshold
Nocardia neocaledoniensis	strain=DSM 44717	GCA_003182135.1	236511	236511	type	True	74.8436	205	2957	95	below_threshold
Nocardia neocaledoniensis	strain=NBRC 108232	GCA_007990735.1	236511	236511	type	True	74.789	197	2957	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:13,552] [INFO] DFAST Taxonomy check result was written to GCF_019039035.1_ASM1903903v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:13,552] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:13,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:13,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43d9129a-420c-4c5a-858c-7423ad91e1c6/dqc_reference/checkm_data
[2024-01-24 12:01:13,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:13,635] [INFO] Task started: CheckM
[2024-01-24 12:01:13,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019039035.1_ASM1903903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019039035.1_ASM1903903v1_genomic.fna/checkm_input GCF_019039035.1_ASM1903903v1_genomic.fna/checkm_result
[2024-01-24 12:05:07,590] [INFO] Task succeeded: CheckM
[2024-01-24 12:05:07,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:05:07,621] [INFO] ===== Completeness check finished =====
[2024-01-24 12:05:07,621] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:05:07,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019039035.1_ASM1903903v1_genomic.fna/markers.fasta)
[2024-01-24 12:05:07,622] [INFO] Task started: Blastn
[2024-01-24 12:05:07,622] [INFO] Running command: blastn -query GCF_019039035.1_ASM1903903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43d9129a-420c-4c5a-858c-7423ad91e1c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019039035.1_ASM1903903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:08,813] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:08,819] [INFO] Selected 19 target genomes.
[2024-01-24 12:05:08,820] [INFO] Target genome list was writen to GCF_019039035.1_ASM1903903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:05:08,891] [INFO] Task started: fastANI
[2024-01-24 12:05:08,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f6c87df-9bbb-4309-a704-c67ab6d77011/GCF_019039035.1_ASM1903903v1_genomic.fna.gz --refList GCF_019039035.1_ASM1903903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019039035.1_ASM1903903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:05:53,081] [INFO] Task succeeded: fastANI
[2024-01-24 12:05:53,101] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:05:53,102] [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_003600865.1	s__Corallococcus sp003600865	99.5122	2866	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.50	99.50	0.97	0.97	2	conclusive
GCA_016458225.1	s__Corallococcus sp016458225	93.4398	2638	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611675.1	s__Corallococcus sp003611675	82.6956	1565	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309135.1	s__Corallococcus sp017309135	82.6874	1722	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909145.1	s__Corallococcus sp009909145	82.6865	1746	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	99.47	99.47	0.98	0.98	2	-
GCF_014930455.1	s__Corallococcus sp014930455	82.6649	1683	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612165.1	s__Corallococcus aberystwythensis	82.6261	1580	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611585.1	s__Corallococcus exercitus	82.6186	1568	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	96.95	95.08	0.87	0.82	3	-
GCF_000255295.1	s__Corallococcus coralloides	82.583	1735	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	95.87	95.41	0.89	0.88	6	-
GCF_017301735.1	s__Myxococcus sp017301735	82.1024	1833	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305895.1	s__Myxococcus macrosporus	82.0203	1656	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.54	98.54	0.93	0.93	2	-
GCF_010894435.1	s__Myxococcus trucidator	81.9841	1788	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	81.9493	1693	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656495.1	s__Myxococcus sp014656495	81.9397	1592	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111765.1	s__Myxococcus fulvus	81.8016	1755	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.03	95.70	0.96	0.91	4	-
GCF_000280925.3	s__Myxococcus hansupus	81.6928	1635	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331735.1	s__Myxococcus stipitatus	81.6889	1710	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013336725.1	s__Myxococcus sp013336725	81.5688	1758	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.23	98.12	0.95	0.94	5	-
GCF_010894455.1	s__Myxococcus eversor	81.5441	1767	2957	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.18	99.18	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:05:53,103] [INFO] GTDB search result was written to GCF_019039035.1_ASM1903903v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:05:53,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:05:53,108] [INFO] DFAST_QC result json was written to GCF_019039035.1_ASM1903903v1_genomic.fna/dqc_result.json
[2024-01-24 12:05:53,109] [INFO] DFAST_QC completed!
[2024-01-24 12:05:53,109] [INFO] Total running time: 0h6m18s