[2023-06-30 16:39:53,287] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:39:53,290] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:39:53,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a73b9f8-db53-4ff5-a829-29c624db1f84/dqc_reference
[2023-06-30 16:39:54,495] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:39:54,496] [INFO] Task started: Prodigal
[2023-06-30 16:39:54,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg38dd395e-404a-41e8-a5ee-fd61f8d76d11/GCA_016188005.1_ASM1618800v1_genomic.fna.gz | prodigal -d GCA_016188005.1_ASM1618800v1_genomic.fna/cds.fna -a GCA_016188005.1_ASM1618800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:40:08,575] [INFO] Task succeeded: Prodigal
[2023-06-30 16:40:08,575] [INFO] Task started: HMMsearch
[2023-06-30 16:40:08,575] [INFO] Running command: hmmsearch --tblout GCA_016188005.1_ASM1618800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a73b9f8-db53-4ff5-a829-29c624db1f84/dqc_reference/reference_markers.hmm GCA_016188005.1_ASM1618800v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:40:08,807] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:40:08,808] [INFO] Found 6/6 markers.
[2023-06-30 16:40:08,853] [INFO] Query marker FASTA was written to GCA_016188005.1_ASM1618800v1_genomic.fna/markers.fasta
[2023-06-30 16:40:08,853] [INFO] Task started: Blastn
[2023-06-30 16:40:08,853] [INFO] Running command: blastn -query GCA_016188005.1_ASM1618800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a73b9f8-db53-4ff5-a829-29c624db1f84/dqc_reference/reference_markers.fasta -out GCA_016188005.1_ASM1618800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:40:09,480] [INFO] Task succeeded: Blastn
[2023-06-30 16:40:09,483] [INFO] Selected 25 target genomes.
[2023-06-30 16:40:09,484] [INFO] Target genome list was writen to GCA_016188005.1_ASM1618800v1_genomic.fna/target_genomes.txt
[2023-06-30 16:40:09,486] [INFO] Task started: fastANI
[2023-06-30 16:40:09,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg38dd395e-404a-41e8-a5ee-fd61f8d76d11/GCA_016188005.1_ASM1618800v1_genomic.fna.gz --refList GCA_016188005.1_ASM1618800v1_genomic.fna/target_genomes.txt --output GCA_016188005.1_ASM1618800v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:40:26,660] [INFO] Task succeeded: fastANI
[2023-06-30 16:40:26,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a73b9f8-db53-4ff5-a829-29c624db1f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:40:26,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a73b9f8-db53-4ff5-a829-29c624db1f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:40:26,678] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:40:26,678] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:40:26,678] [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
Geobacter pickeringii	strain=G13	GCA_000817955.1	345632	345632	type	True	75.6251	56	1722	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.1993	76	1722	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	75.1873	78	1722	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	75.1618	84	1722	95	below_threshold
Limimonas halophila	strain=DSM 25584	GCA_900100655.1	1082479	1082479	type	True	75.1421	99	1722	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	75.0396	130	1722	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	75.0105	132	1722	95	below_threshold
Limnochorda pilosa	strain=HC45	GCA_001544015.1	1555112	1555112	type	True	74.9962	81	1722	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	74.9647	65	1722	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	74.9639	65	1722	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	74.9438	77	1722	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	74.9344	123	1722	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	74.8881	90	1722	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	74.7982	126	1722	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	74.7858	83	1722	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.7518	229	1722	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	74.7173	159	1722	95	below_threshold
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	74.6868	129	1722	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.6845	238	1722	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	74.6084	183	1722	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	74.6075	183	1722	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	74.5763	64	1722	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:40:26,680] [INFO] DFAST Taxonomy check result was written to GCA_016188005.1_ASM1618800v1_genomic.fna/tc_result.tsv
[2023-06-30 16:40:26,681] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:40:26,681] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:40:26,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a73b9f8-db53-4ff5-a829-29c624db1f84/dqc_reference/checkm_data
[2023-06-30 16:40:26,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:40:26,733] [INFO] Task started: CheckM
[2023-06-30 16:40:26,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016188005.1_ASM1618800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016188005.1_ASM1618800v1_genomic.fna/checkm_input GCA_016188005.1_ASM1618800v1_genomic.fna/checkm_result
[2023-06-30 16:41:19,913] [INFO] Task succeeded: CheckM
[2023-06-30 16:41:19,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:41:19,935] [INFO] ===== Completeness check finished =====
[2023-06-30 16:41:19,935] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:41:19,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016188005.1_ASM1618800v1_genomic.fna/markers.fasta)
[2023-06-30 16:41:19,935] [INFO] Task started: Blastn
[2023-06-30 16:41:19,935] [INFO] Running command: blastn -query GCA_016188005.1_ASM1618800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a73b9f8-db53-4ff5-a829-29c624db1f84/dqc_reference/reference_markers_gtdb.fasta -out GCA_016188005.1_ASM1618800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:41:20,868] [INFO] Task succeeded: Blastn
[2023-06-30 16:41:20,871] [INFO] Selected 11 target genomes.
[2023-06-30 16:41:20,871] [INFO] Target genome list was writen to GCA_016188005.1_ASM1618800v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:41:20,872] [INFO] Task started: fastANI
[2023-06-30 16:41:20,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg38dd395e-404a-41e8-a5ee-fd61f8d76d11/GCA_016188005.1_ASM1618800v1_genomic.fna.gz --refList GCA_016188005.1_ASM1618800v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016188005.1_ASM1618800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:41:30,942] [INFO] Task succeeded: fastANI
[2023-06-30 16:41:30,951] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:41:30,951] [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_016188005.1	s__UBA12499 sp016188005	100.0	1716	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001788415.1	s__UBA12499 sp001788415	90.3095	927	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177555.1	s__UBA12499 sp016177555	86.8008	482	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	97.25	97.17	0.72	0.67	3	-
GCA_001788395.1	s__UBA12499 sp001788395	85.853	957	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__UBA12499	95.0	99.38	99.38	0.91	0.91	2	-
GCA_016179165.1	s__AR37 sp016179165	78.5003	371	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220345.1	s__AR37 sp003220345	78.3344	500	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR37	95.0	98.45	98.45	0.87	0.87	2	-
GCA_016179875.1	s__GWA2-73-35 sp016179875	78.0731	466	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__GWA2-73-35	95.0	98.74	98.74	0.82	0.82	2	-
GCA_001788495.1	s__GWA2-73-35 sp001788495	77.6992	511	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__GWA2-73-35	95.0	99.58	99.46	0.87	0.84	4	-
GCA_001790205.1	s__GWA2-73-35 sp001790205	77.59	436	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__GWA2-73-35	95.0	99.55	99.55	0.88	0.88	2	-
GCA_003220265.1	s__AR5 sp003220265	77.2606	505	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003221455.1	s__AR9 sp003221455	77.1278	310	1722	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:41:30,953] [INFO] GTDB search result was written to GCA_016188005.1_ASM1618800v1_genomic.fna/result_gtdb.tsv
[2023-06-30 16:41:30,954] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:41:30,958] [INFO] DFAST_QC result json was written to GCA_016188005.1_ASM1618800v1_genomic.fna/dqc_result.json
[2023-06-30 16:41:30,958] [INFO] DFAST_QC completed!
[2023-06-30 16:41:30,958] [INFO] Total running time: 0h1m38s