[2023-03-15 12:44:24,470] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg250f6d1c-df63-4f9e-9f01-92b7db4f11b3/dqc_reference
[2023-03-15 12:44:26,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,209] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,209] [INFO] Running command: cat /var/lib/cwl/stg7a7584a2-4b3d-4a24-8808-736ac128bc39/OceanDNA-b2796.fa | prodigal -d OceanDNA-b2796/cds.fna -a OceanDNA-b2796/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:40,711] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:40,711] [INFO] Task started: HMMsearch
[2023-03-15 12:44:40,711] [INFO] Running command: hmmsearch --tblout OceanDNA-b2796/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg250f6d1c-df63-4f9e-9f01-92b7db4f11b3/dqc_reference/reference_markers.hmm OceanDNA-b2796/protein.faa > /dev/null
[2023-03-15 12:44:40,971] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:40,972] [INFO] Found 6/6 markers.
[2023-03-15 12:44:40,988] [INFO] Query marker FASTA was written to OceanDNA-b2796/markers.fasta
[2023-03-15 12:44:40,989] [INFO] Task started: Blastn
[2023-03-15 12:44:40,989] [INFO] Running command: blastn -query OceanDNA-b2796/markers.fasta -db /var/lib/cwl/stg250f6d1c-df63-4f9e-9f01-92b7db4f11b3/dqc_reference/reference_markers.fasta -out OceanDNA-b2796/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:42,195] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:42,196] [INFO] Selected 27 target genomes.
[2023-03-15 12:44:42,196] [INFO] Target genome list was writen to OceanDNA-b2796/target_genomes.txt
[2023-03-15 12:44:42,213] [INFO] Task started: fastANI
[2023-03-15 12:44:42,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a7584a2-4b3d-4a24-8808-736ac128bc39/OceanDNA-b2796.fa --refList OceanDNA-b2796/target_genomes.txt --output OceanDNA-b2796/fastani_result.tsv --threads 1
[2023-03-15 12:44:58,950] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:58,950] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg250f6d1c-df63-4f9e-9f01-92b7db4f11b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:58,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg250f6d1c-df63-4f9e-9f01-92b7db4f11b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:58,965] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:58,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:44:58,966] [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
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	81.1357	433	796	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	80.7584	405	796	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	80.0236	374	796	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	79.993	378	796	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	79.2311	377	796	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.1237	396	796	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	79.0952	365	796	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	79.058	353	796	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	79.0535	349	796	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	79.0501	378	796	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.9946	354	796	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	78.9415	312	796	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	78.9067	313	796	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	78.901	338	796	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.8807	329	796	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.8332	316	796	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.7928	341	796	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.7924	327	796	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.735	340	796	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	78.6956	340	796	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.6769	325	796	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	78.6336	315	796	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	78.5399	316	796	95	below_threshold
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	78.4911	265	796	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	78.4622	285	796	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	78.3573	286	796	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	78.1824	339	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:44:58,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2796/tc_result.tsv
[2023-03-15 12:44:58,966] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:58,966] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:58,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg250f6d1c-df63-4f9e-9f01-92b7db4f11b3/dqc_reference/checkm_data
[2023-03-15 12:44:58,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:59,020] [INFO] Task started: CheckM
[2023-03-15 12:44:59,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2796/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2796/checkm_input OceanDNA-b2796/checkm_result
[2023-03-15 12:45:44,907] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:44,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:44,909] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:44,909] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:44,910] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2796/markers.fasta)
[2023-03-15 12:45:44,911] [INFO] Task started: Blastn
[2023-03-15 12:45:44,911] [INFO] Running command: blastn -query OceanDNA-b2796/markers.fasta -db /var/lib/cwl/stg250f6d1c-df63-4f9e-9f01-92b7db4f11b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2796/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:46,843] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:46,844] [INFO] Selected 19 target genomes.
[2023-03-15 12:45:46,844] [INFO] Target genome list was writen to OceanDNA-b2796/target_genomes_gtdb.txt
[2023-03-15 12:45:47,004] [INFO] Task started: fastANI
[2023-03-15 12:45:47,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a7584a2-4b3d-4a24-8808-736ac128bc39/OceanDNA-b2796.fa --refList OceanDNA-b2796/target_genomes_gtdb.txt --output OceanDNA-b2796/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:58,622] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:58,634] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:45:58,634] [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_002325245.1	s__Pseudolysinimonas sp002325245	99.9625	771	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	99.78	99.17	0.96	0.89	14	conclusive
GCA_905479755.1	s__Pseudolysinimonas sp905479755	88.0943	635	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	81.1421	433	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	80.8069	430	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365275.1	s__Protaetiibacter larvae	80.7266	407	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308515.1	s__Pseudolysinimonas sp017308515	80.7004	465	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517535.1	s__Schumannella sp006517535	80.6539	432	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014483895.1	s__Protaetiibacter sp014483895	80.6426	435	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216815.1	s__Protaetiibacter sp004216815	80.5485	429	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408685.1	s__Schumannella luteola	80.5167	445	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	80.5079	423	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006517435.1	s__Schumannella sp006517435	80.4882	429	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003243275.1	s__Protaetiibacter sp003243275	80.4697	411	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011751865.2	s__Protaetiibacter sp011751905	80.3183	379	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	98.78	98.78	0.94	0.94	2	-
GCF_014653215.1	s__Pseudolysinimonas yzui	80.2729	434	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502445.1	s__Yonghaparkia sp005502445	79.7535	337	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.7295	401	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576405.1	s__Clavibacter sp003576405	78.9643	302	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.88	99.88	0.93	0.93	2	-
GCF_011057645.1	s__Marisediminicola senii	78.6764	325	796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marisediminicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:45:58,634] [INFO] GTDB search result was written to OceanDNA-b2796/result_gtdb.tsv
[2023-03-15 12:45:58,634] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:58,637] [INFO] DFAST_QC result json was written to OceanDNA-b2796/dqc_result.json
[2023-03-15 12:45:58,637] [INFO] DFAST_QC completed!
[2023-03-15 12:45:58,637] [INFO] Total running time: 0h1m34s