[2023-03-18 08:31:56,312] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,312] [INFO] DQC Reference Directory: /var/lib/cwl/stgf370b3e8-5134-4a96-8f9c-a25d2b931362/dqc_reference
[2023-03-18 08:31:57,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,432] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,432] [INFO] Running command: cat /var/lib/cwl/stga6dd0a1e-4a8a-45ac-903e-ad22482ae24f/OceanDNA-b22017.fa | prodigal -d OceanDNA-b22017/cds.fna -a OceanDNA-b22017/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:22,573] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:22,573] [INFO] Task started: HMMsearch
[2023-03-18 08:32:22,573] [INFO] Running command: hmmsearch --tblout OceanDNA-b22017/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf370b3e8-5134-4a96-8f9c-a25d2b931362/dqc_reference/reference_markers.hmm OceanDNA-b22017/protein.faa > /dev/null
[2023-03-18 08:32:22,835] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:22,835] [INFO] Found 6/6 markers.
[2023-03-18 08:32:22,872] [INFO] Query marker FASTA was written to OceanDNA-b22017/markers.fasta
[2023-03-18 08:32:22,872] [INFO] Task started: Blastn
[2023-03-18 08:32:22,872] [INFO] Running command: blastn -query OceanDNA-b22017/markers.fasta -db /var/lib/cwl/stgf370b3e8-5134-4a96-8f9c-a25d2b931362/dqc_reference/reference_markers.fasta -out OceanDNA-b22017/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:23,455] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:23,456] [INFO] Selected 29 target genomes.
[2023-03-18 08:32:23,456] [INFO] Target genome list was writen to OceanDNA-b22017/target_genomes.txt
[2023-03-18 08:32:23,470] [INFO] Task started: fastANI
[2023-03-18 08:32:23,470] [INFO] Running command: fastANI --query /var/lib/cwl/stga6dd0a1e-4a8a-45ac-903e-ad22482ae24f/OceanDNA-b22017.fa --refList OceanDNA-b22017/target_genomes.txt --output OceanDNA-b22017/fastani_result.tsv --threads 1
[2023-03-18 08:32:43,616] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:43,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf370b3e8-5134-4a96-8f9c-a25d2b931362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:43,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf370b3e8-5134-4a96-8f9c-a25d2b931362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:43,626] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:43,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:32:43,626] [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
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8888	109	1341	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.8813	70	1341	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.856	95	1341	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	74.8384	77	1341	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8053	95	1341	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	74.7843	83	1341	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	74.7806	60	1341	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7645	170	1341	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7604	119	1341	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	74.7238	75	1341	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	74.7102	113	1341	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	74.7046	82	1341	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	74.6567	82	1341	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	74.6247	54	1341	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	74.6053	72	1341	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	74.6028	102	1341	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:32:43,627] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22017/tc_result.tsv
[2023-03-18 08:32:43,627] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:43,627] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:43,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf370b3e8-5134-4a96-8f9c-a25d2b931362/dqc_reference/checkm_data
[2023-03-18 08:32:43,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:43,674] [INFO] Task started: CheckM
[2023-03-18 08:32:43,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22017/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22017/checkm_input OceanDNA-b22017/checkm_result
[2023-03-18 08:33:44,568] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:44,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:33:44,572] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:44,572] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:44,573] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22017/markers.fasta)
[2023-03-18 08:33:44,573] [INFO] Task started: Blastn
[2023-03-18 08:33:44,573] [INFO] Running command: blastn -query OceanDNA-b22017/markers.fasta -db /var/lib/cwl/stgf370b3e8-5134-4a96-8f9c-a25d2b931362/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22017/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:45,421] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:45,423] [INFO] Selected 36 target genomes.
[2023-03-18 08:33:45,423] [INFO] Target genome list was writen to OceanDNA-b22017/target_genomes_gtdb.txt
[2023-03-18 08:33:45,653] [INFO] Task started: fastANI
[2023-03-18 08:33:45,653] [INFO] Running command: fastANI --query /var/lib/cwl/stga6dd0a1e-4a8a-45ac-903e-ad22482ae24f/OceanDNA-b22017.fa --refList OceanDNA-b22017/target_genomes_gtdb.txt --output OceanDNA-b22017/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:34:12,425] [INFO] Task succeeded: fastANI
[2023-03-18 08:34:12,438] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:34:12,439] [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_016935485.1	s__JAFGQW01 sp016935485	75.2234	79	1341	d__Bacteria;p__Planctomycetota;c__JAFGQW01;o__JAFGQW01;f__JAFGQW01;g__JAFGQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999985.1	s__JAGNKU01 sp017999985	75.1485	51	1341	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__JAGNKU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793245.1	s__JADKAF01 sp016793245	75.0996	149	1341	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719295.1	s__JADKAF01 sp016719295	75.0344	162	1341	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	75.0276	141	1341	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213895.1	s__JACQZJ01 sp016213895	75.0048	82	1341	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__JADJEK01;g__JACQZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697015.1	s__J023 sp003697015	74.9628	74	1341	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	74.9625	105	1341	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792665.1	s__WYBB01 sp016792665	74.944	96	1341	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__WYBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795345.1	s__JAEUHO01 sp016795345	74.9416	114	1341	d__Bacteria;p__Planctomycetota;c__PLA2;o__PLA2;f__JAEUHO01;g__JAEUHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524785.1	s__GCA-2686945 sp011524785	74.9094	50	1341	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197205.1	s__JACPWG01 sp016197205	74.8767	98	1341	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__JACPWG01;g__JACPWG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235155.1	s__JACRLW01 sp016235155	74.8613	109	1341	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JACRLW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	74.8484	97	1341	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610895.1	s__Paludisphaera sp001610895	74.79	77	1341	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	74.7806	60	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424125.1	s__Cellulomonas sp001424125	74.7747	66	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	74.7643	79	1341	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087625.1	s__Aquisphaera giovannonii	74.7577	119	1341	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	74.7079	83	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359775.1	s__Cellulomonas humilata	74.6019	73	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	74.5994	103	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	74.5882	57	1341	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:34:12,439] [INFO] GTDB search result was written to OceanDNA-b22017/result_gtdb.tsv
[2023-03-18 08:34:12,439] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:34:12,441] [INFO] DFAST_QC result json was written to OceanDNA-b22017/dqc_result.json
[2023-03-18 08:34:12,441] [INFO] DFAST_QC completed!
[2023-03-18 08:34:12,441] [INFO] Total running time: 0h2m16s