[2023-03-15 08:01:24,673] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:01:24,673] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:01:24,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b730b0e-4530-44c4-8881-9305ddaf6d33/dqc_reference
[2023-03-15 08:01:25,908] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:01:25,909] [INFO] Task started: Prodigal
[2023-03-15 08:01:25,909] [INFO] Running command: cat /var/lib/cwl/stg2652f88d-9361-4adb-9ff1-5fbdcc423f35/OceanDNA-b32793.fa | prodigal -d OceanDNA-b32793/cds.fna -a OceanDNA-b32793/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:01:50,238] [INFO] Task succeeded: Prodigal
[2023-03-15 08:01:50,238] [INFO] Task started: HMMsearch
[2023-03-15 08:01:50,238] [INFO] Running command: hmmsearch --tblout OceanDNA-b32793/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b730b0e-4530-44c4-8881-9305ddaf6d33/dqc_reference/reference_markers.hmm OceanDNA-b32793/protein.faa > /dev/null
[2023-03-15 08:01:50,509] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:01:50,510] [INFO] Found 6/6 markers.
[2023-03-15 08:01:50,534] [INFO] Query marker FASTA was written to OceanDNA-b32793/markers.fasta
[2023-03-15 08:01:50,536] [INFO] Task started: Blastn
[2023-03-15 08:01:50,536] [INFO] Running command: blastn -query OceanDNA-b32793/markers.fasta -db /var/lib/cwl/stg8b730b0e-4530-44c4-8881-9305ddaf6d33/dqc_reference/reference_markers.fasta -out OceanDNA-b32793/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:01:51,523] [INFO] Task succeeded: Blastn
[2023-03-15 08:01:51,524] [INFO] Selected 31 target genomes.
[2023-03-15 08:01:51,524] [INFO] Target genome list was writen to OceanDNA-b32793/target_genomes.txt
[2023-03-15 08:01:51,547] [INFO] Task started: fastANI
[2023-03-15 08:01:51,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg2652f88d-9361-4adb-9ff1-5fbdcc423f35/OceanDNA-b32793.fa --refList OceanDNA-b32793/target_genomes.txt --output OceanDNA-b32793/fastani_result.tsv --threads 1
[2023-03-15 08:02:15,983] [INFO] Task succeeded: fastANI
[2023-03-15 08:02:15,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b730b0e-4530-44c4-8881-9305ddaf6d33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:02:15,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b730b0e-4530-44c4-8881-9305ddaf6d33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:02:16,010] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:02:16,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:02:16,011] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.0149	203	1361	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.8521	228	1361	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.834	237	1361	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.8235	165	1361	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.7283	297	1361	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.6825	236	1361	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.66	230	1361	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.6402	341	1361	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.608	347	1361	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.6025	267	1361	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.5963	269	1361	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.585	227	1361	95	below_threshold
Blastochloris viridis	strain=DSM 133	GCA_001548155.2	1079	1079	type	True	76.5695	163	1361	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.5527	169	1361	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	76.5304	161	1361	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.5173	228	1361	95	below_threshold
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	76.5105	179	1361	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.5073	235	1361	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.4424	246	1361	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	76.3658	133	1361	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	76.3135	205	1361	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.312	192	1361	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_004362995.1	1264899	1264899	type	True	76.2801	204	1361	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.22	153	1361	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1654	119	1361	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1204	201	1361	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	76.0448	179	1361	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	76.0428	185	1361	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	75.9962	129	1361	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.8296	95	1361	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.7721	114	1361	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:02:16,011] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32793/tc_result.tsv
[2023-03-15 08:02:16,011] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:02:16,011] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:02:16,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b730b0e-4530-44c4-8881-9305ddaf6d33/dqc_reference/checkm_data
[2023-03-15 08:02:16,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:02:16,018] [INFO] Task started: CheckM
[2023-03-15 08:02:16,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32793/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32793/checkm_input OceanDNA-b32793/checkm_result
[2023-03-15 08:03:16,118] [INFO] Task succeeded: CheckM
[2023-03-15 08:03:16,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:03:16,121] [INFO] ===== Completeness check finished =====
[2023-03-15 08:03:16,121] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:03:16,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32793/markers.fasta)
[2023-03-15 08:03:16,123] [INFO] Task started: Blastn
[2023-03-15 08:03:16,123] [INFO] Running command: blastn -query OceanDNA-b32793/markers.fasta -db /var/lib/cwl/stg8b730b0e-4530-44c4-8881-9305ddaf6d33/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32793/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:03:18,138] [INFO] Task succeeded: Blastn
[2023-03-15 08:03:18,139] [INFO] Selected 30 target genomes.
[2023-03-15 08:03:18,139] [INFO] Target genome list was writen to OceanDNA-b32793/target_genomes_gtdb.txt
[2023-03-15 08:03:18,201] [INFO] Task started: fastANI
[2023-03-15 08:03:18,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg2652f88d-9361-4adb-9ff1-5fbdcc423f35/OceanDNA-b32793.fa --refList OceanDNA-b32793/target_genomes_gtdb.txt --output OceanDNA-b32793/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:03:49,062] [INFO] Task succeeded: fastANI
[2023-03-15 08:03:49,078] [INFO] Found 30 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:03:49,079] [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_002721365.1	s__GCA-2721365 sp002721365	99.8602	1186	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2721365;f__GCA-2721365;g__GCA-2721365	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_006739055.1	s__Stella vacuolata	77.1249	285	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240685.1	s__Reyranella sp018240685	76.873	177	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.8516	227	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	76.844	236	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364825.1	s__Azospirillum sp008364825	76.8412	240	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.23	95.23	0.77	0.77	2	-
GCA_016869145.1	s__VGEU01 sp016869145	76.8337	196	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.7651	199	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116095.1	s__Azospirillum sp003116095	76.7538	280	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.7416	209	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003675.1	s__JABDIP01 sp013003675	76.7403	159	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.7225	298	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	76.6948	270	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014643535.1	s__Aliidongia dinghuensis	76.6923	236	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Aliidongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177515.1	s__Azospirillum oryzae_A	76.6835	263	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429625.1	s__Azospirillum halopraeferens	76.6669	229	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	76.6599	267	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	76.6265	287	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.6144	347	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006738645.1	s__Stella humosa	76.6015	267	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.5681	169	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.5527	169	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590945.1	s__Zavarzinia sp003590945	76.5048	223	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869285.1	s__SHVZ01 sp016869285	76.4625	197	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	76.4187	167	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185145.1	s__Reyranella sp016185145	76.3829	227	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	76.113	147	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	76.0864	209	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966125.1	s__Azospirillum griseum	76.02	167	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666805.1	s__PTKB01 sp018666805	75.7536	77	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
--------------------------------------------------------------------------------
[2023-03-15 08:03:49,079] [INFO] GTDB search result was written to OceanDNA-b32793/result_gtdb.tsv
[2023-03-15 08:03:49,079] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:03:49,082] [INFO] DFAST_QC result json was written to OceanDNA-b32793/dqc_result.json
[2023-03-15 08:03:49,082] [INFO] DFAST_QC completed!
[2023-03-15 08:03:49,082] [INFO] Total running time: 0h2m24s