[2023-03-18 01:59:39,746] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,748] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fd1fe6d-32c8-49ee-bf79-1ceef4941b38/dqc_reference
[2023-03-18 01:59:40,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,952] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,952] [INFO] Running command: cat /var/lib/cwl/stg31511676-a875-4d4d-af68-aff2bcac8644/OceanDNA-b30458.fa | prodigal -d OceanDNA-b30458/cds.fna -a OceanDNA-b30458/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:00:07,719] [INFO] Task succeeded: Prodigal
[2023-03-18 02:00:07,719] [INFO] Task started: HMMsearch
[2023-03-18 02:00:07,719] [INFO] Running command: hmmsearch --tblout OceanDNA-b30458/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fd1fe6d-32c8-49ee-bf79-1ceef4941b38/dqc_reference/reference_markers.hmm OceanDNA-b30458/protein.faa > /dev/null
[2023-03-18 02:00:07,937] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:00:07,938] [INFO] Found 6/6 markers.
[2023-03-18 02:00:07,965] [INFO] Query marker FASTA was written to OceanDNA-b30458/markers.fasta
[2023-03-18 02:00:07,966] [INFO] Task started: Blastn
[2023-03-18 02:00:07,966] [INFO] Running command: blastn -query OceanDNA-b30458/markers.fasta -db /var/lib/cwl/stg5fd1fe6d-32c8-49ee-bf79-1ceef4941b38/dqc_reference/reference_markers.fasta -out OceanDNA-b30458/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:08,847] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:08,903] [INFO] Selected 23 target genomes.
[2023-03-18 02:00:08,903] [INFO] Target genome list was writen to OceanDNA-b30458/target_genomes.txt
[2023-03-18 02:00:08,919] [INFO] Task started: fastANI
[2023-03-18 02:00:08,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg31511676-a875-4d4d-af68-aff2bcac8644/OceanDNA-b30458.fa --refList OceanDNA-b30458/target_genomes.txt --output OceanDNA-b30458/fastani_result.tsv --threads 1
[2023-03-18 02:00:27,703] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:27,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fd1fe6d-32c8-49ee-bf79-1ceef4941b38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:27,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fd1fe6d-32c8-49ee-bf79-1ceef4941b38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:27,716] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:00:27,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:00:27,717] [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
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	89.7295	1180	1344	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	89.6623	1188	1344	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	79.1318	598	1344	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.6674	529	1344	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.5662	556	1344	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.3985	551	1344	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	78.3972	479	1344	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.3663	509	1344	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.3365	469	1344	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.2806	454	1344	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.2743	465	1344	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.2118	461	1344	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.1789	409	1344	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	78.0912	427	1344	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	78.0323	388	1344	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.9279	461	1344	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.765	401	1344	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.7248	387	1344	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5453	333	1344	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	77.4755	362	1344	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0688	297	1344	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.0109	356	1344	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.8601	267	1344	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:00:27,719] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30458/tc_result.tsv
[2023-03-18 02:00:27,721] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:27,721] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:27,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fd1fe6d-32c8-49ee-bf79-1ceef4941b38/dqc_reference/checkm_data
[2023-03-18 02:00:27,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:27,798] [INFO] Task started: CheckM
[2023-03-18 02:00:27,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30458/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30458/checkm_input OceanDNA-b30458/checkm_result
[2023-03-18 02:01:37,633] [INFO] Task succeeded: CheckM
[2023-03-18 02:01:37,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 02:01:37,688] [INFO] ===== Completeness check finished =====
[2023-03-18 02:01:37,688] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:01:37,688] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30458/markers.fasta)
[2023-03-18 02:01:37,689] [INFO] Task started: Blastn
[2023-03-18 02:01:37,689] [INFO] Running command: blastn -query OceanDNA-b30458/markers.fasta -db /var/lib/cwl/stg5fd1fe6d-32c8-49ee-bf79-1ceef4941b38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30458/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:01:39,311] [INFO] Task succeeded: Blastn
[2023-03-18 02:01:39,321] [INFO] Selected 11 target genomes.
[2023-03-18 02:01:39,321] [INFO] Target genome list was writen to OceanDNA-b30458/target_genomes_gtdb.txt
[2023-03-18 02:01:39,334] [INFO] Task started: fastANI
[2023-03-18 02:01:39,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg31511676-a875-4d4d-af68-aff2bcac8644/OceanDNA-b30458.fa --refList OceanDNA-b30458/target_genomes_gtdb.txt --output OceanDNA-b30458/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:01:49,450] [INFO] Task succeeded: fastANI
[2023-03-18 02:01:49,457] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:01:49,457] [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
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	89.7245	1188	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	89.6623	1188	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	87.273	1022	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	85.0135	1025	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	79.1198	600	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.9361	601	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	78.8414	528	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_013282155.1	s__Sulfitobacter sp013282155	78.7147	509	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.5662	556	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_009857745.1	s__Thalassobius mangrovi	78.359	510	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	78.1563	483	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:01:49,462] [INFO] GTDB search result was written to OceanDNA-b30458/result_gtdb.tsv
[2023-03-18 02:01:49,471] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:01:49,476] [INFO] DFAST_QC result json was written to OceanDNA-b30458/dqc_result.json
[2023-03-18 02:01:49,476] [INFO] DFAST_QC completed!
[2023-03-18 02:01:49,477] [INFO] Total running time: 0h2m10s