[2023-06-28 02:00:14,001] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:00:14,005] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:00:14,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg54f40eac-051c-4d68-9761-ea5f86a25136/dqc_reference
[2023-06-28 02:00:15,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:00:15,759] [INFO] Task started: Prodigal
[2023-06-28 02:00:15,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg700589d9-5adc-45f6-8b57-be0736cfd54f/GCA_019310435.1_ASM1931043v1_genomic.fna.gz | prodigal -d GCA_019310435.1_ASM1931043v1_genomic.fna/cds.fna -a GCA_019310435.1_ASM1931043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:00:27,409] [INFO] Task succeeded: Prodigal
[2023-06-28 02:00:27,409] [INFO] Task started: HMMsearch
[2023-06-28 02:00:27,409] [INFO] Running command: hmmsearch --tblout GCA_019310435.1_ASM1931043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54f40eac-051c-4d68-9761-ea5f86a25136/dqc_reference/reference_markers.hmm GCA_019310435.1_ASM1931043v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:00:27,777] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:00:27,778] [INFO] Found 6/6 markers.
[2023-06-28 02:00:27,819] [INFO] Query marker FASTA was written to GCA_019310435.1_ASM1931043v1_genomic.fna/markers.fasta
[2023-06-28 02:00:27,819] [INFO] Task started: Blastn
[2023-06-28 02:00:27,819] [INFO] Running command: blastn -query GCA_019310435.1_ASM1931043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f40eac-051c-4d68-9761-ea5f86a25136/dqc_reference/reference_markers.fasta -out GCA_019310435.1_ASM1931043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:00:28,557] [INFO] Task succeeded: Blastn
[2023-06-28 02:00:28,562] [INFO] Selected 20 target genomes.
[2023-06-28 02:00:28,562] [INFO] Target genome list was writen to GCA_019310435.1_ASM1931043v1_genomic.fna/target_genomes.txt
[2023-06-28 02:00:28,566] [INFO] Task started: fastANI
[2023-06-28 02:00:28,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg700589d9-5adc-45f6-8b57-be0736cfd54f/GCA_019310435.1_ASM1931043v1_genomic.fna.gz --refList GCA_019310435.1_ASM1931043v1_genomic.fna/target_genomes.txt --output GCA_019310435.1_ASM1931043v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:00:46,924] [INFO] Task succeeded: fastANI
[2023-06-28 02:00:46,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54f40eac-051c-4d68-9761-ea5f86a25136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:00:46,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54f40eac-051c-4d68-9761-ea5f86a25136/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:00:46,937] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:00:46,937] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 02:00:46,937] [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
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.4763	102	1371	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.224	177	1371	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.0557	99	1371	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.0154	121	1371	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	75.0033	92	1371	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	74.9923	79	1371	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.962	108	1371	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.9355	162	1371	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	74.9162	93	1371	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.9042	175	1371	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8964	246	1371	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.885	255	1371	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	74.8586	203	1371	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	74.8396	97	1371	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 02:00:46,940] [INFO] DFAST Taxonomy check result was written to GCA_019310435.1_ASM1931043v1_genomic.fna/tc_result.tsv
[2023-06-28 02:00:46,941] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:00:46,941] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:00:46,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54f40eac-051c-4d68-9761-ea5f86a25136/dqc_reference/checkm_data
[2023-06-28 02:00:46,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:00:46,991] [INFO] Task started: CheckM
[2023-06-28 02:00:46,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310435.1_ASM1931043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310435.1_ASM1931043v1_genomic.fna/checkm_input GCA_019310435.1_ASM1931043v1_genomic.fna/checkm_result
[2023-06-28 02:01:24,708] [INFO] Task succeeded: CheckM
[2023-06-28 02:01:24,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:01:24,731] [INFO] ===== Completeness check finished =====
[2023-06-28 02:01:24,731] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:01:24,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310435.1_ASM1931043v1_genomic.fna/markers.fasta)
[2023-06-28 02:01:24,732] [INFO] Task started: Blastn
[2023-06-28 02:01:24,732] [INFO] Running command: blastn -query GCA_019310435.1_ASM1931043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f40eac-051c-4d68-9761-ea5f86a25136/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310435.1_ASM1931043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:01:25,909] [INFO] Task succeeded: Blastn
[2023-06-28 02:01:25,914] [INFO] Selected 23 target genomes.
[2023-06-28 02:01:25,914] [INFO] Target genome list was writen to GCA_019310435.1_ASM1931043v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:01:25,930] [INFO] Task started: fastANI
[2023-06-28 02:01:25,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg700589d9-5adc-45f6-8b57-be0736cfd54f/GCA_019310435.1_ASM1931043v1_genomic.fna.gz --refList GCA_019310435.1_ASM1931043v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310435.1_ASM1931043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:01:42,648] [INFO] Task succeeded: fastANI
[2023-06-28 02:01:42,664] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:01:42,664] [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_002687015.1	s__GCA-2687015 sp002687015	77.1818	260	1371	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	76.8439	234	1371	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.663	349	1371	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696485.1	s__CAADGG01 sp900696485	76.5113	224	1371	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__CAADGG01	95.0	99.84	99.84	0.91	0.91	2	-
GCA_011055735.1	s__DSOP01 sp011055735	76.4782	310	1371	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729515.1	s__GCA-2729515 sp002729515	76.3853	190	1371	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.3182	271	1371	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.1842	212	1371	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220195.1	s__AR8 sp003220195	75.0701	79	1371	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220615.1	s__40CM-68-15 sp003220615	75.0687	95	1371	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__40CM-68-15	95.0	99.09	97.89	0.93	0.88	5	-
GCA_016712565.1	s__JADJQU01 sp016712565	75.0268	67	1371	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852895.1	s__Albitalea terrae	74.9839	68	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Albitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218785.1	s__JACRCY01 sp016218785	74.8178	121	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__JACRCY01;f__JACRCY01;g__JACRCY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:01:42,666] [INFO] GTDB search result was written to GCA_019310435.1_ASM1931043v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:01:42,667] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:01:42,671] [INFO] DFAST_QC result json was written to GCA_019310435.1_ASM1931043v1_genomic.fna/dqc_result.json
[2023-06-28 02:01:42,671] [INFO] DFAST_QC completed!
[2023-06-28 02:01:42,671] [INFO] Total running time: 0h1m29s