[2023-03-17 05:39:41,238] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:39:41,238] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:39:41,238] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fd0e52d-2e30-40bb-8dc9-b98c47d6439c/dqc_reference
[2023-03-17 05:39:42,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:39:42,366] [INFO] Task started: Prodigal
[2023-03-17 05:39:42,366] [INFO] Running command: cat /var/lib/cwl/stgee03a6a6-3129-419f-a29f-23845e6eeeee/OceanDNA-b30061.fa | prodigal -d OceanDNA-b30061/cds.fna -a OceanDNA-b30061/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:40:04,455] [INFO] Task succeeded: Prodigal
[2023-03-17 05:40:04,455] [INFO] Task started: HMMsearch
[2023-03-17 05:40:04,455] [INFO] Running command: hmmsearch --tblout OceanDNA-b30061/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fd0e52d-2e30-40bb-8dc9-b98c47d6439c/dqc_reference/reference_markers.hmm OceanDNA-b30061/protein.faa > /dev/null
[2023-03-17 05:40:04,659] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:40:04,660] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgee03a6a6-3129-419f-a29f-23845e6eeeee/OceanDNA-b30061.fa]
[2023-03-17 05:40:04,683] [INFO] Query marker FASTA was written to OceanDNA-b30061/markers.fasta
[2023-03-17 05:40:04,685] [INFO] Task started: Blastn
[2023-03-17 05:40:04,685] [INFO] Running command: blastn -query OceanDNA-b30061/markers.fasta -db /var/lib/cwl/stg5fd0e52d-2e30-40bb-8dc9-b98c47d6439c/dqc_reference/reference_markers.fasta -out OceanDNA-b30061/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:40:05,287] [INFO] Task succeeded: Blastn
[2023-03-17 05:40:05,287] [INFO] Selected 23 target genomes.
[2023-03-17 05:40:05,288] [INFO] Target genome list was writen to OceanDNA-b30061/target_genomes.txt
[2023-03-17 05:40:05,310] [INFO] Task started: fastANI
[2023-03-17 05:40:05,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgee03a6a6-3129-419f-a29f-23845e6eeeee/OceanDNA-b30061.fa --refList OceanDNA-b30061/target_genomes.txt --output OceanDNA-b30061/fastani_result.tsv --threads 1
[2023-03-17 05:40:19,745] [INFO] Task succeeded: fastANI
[2023-03-17 05:40:19,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fd0e52d-2e30-40bb-8dc9-b98c47d6439c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:40:19,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fd0e52d-2e30-40bb-8dc9-b98c47d6439c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:40:19,758] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:40:19,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:40:19,759] [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
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	77.2305	181	1179	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	77.0605	211	1179	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	77.0468	216	1179	95	below_threshold
Roseobacter ponti	strain=DSM 106830	GCA_012932215.1	1891787	1891787	type	True	76.9606	212	1179	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	76.9334	206	1179	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	76.9198	108	1179	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.7445	123	1179	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.572	175	1179	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.4404	103	1179	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.3639	115	1179	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.3294	91	1179	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	76.3267	120	1179	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.3247	120	1179	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.2956	118	1179	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.1941	97	1179	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	75.9855	76	1179	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	75.9855	76	1179	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	75.9826	63	1179	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	75.9571	111	1179	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	75.9042	95	1179	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	75.8518	54	1179	95	below_threshold
Tropicimonas isoalkanivorans	strain=DSM 19548	GCA_900112335.1	441112	441112	type	True	75.7723	69	1179	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:40:19,759] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30061/tc_result.tsv
[2023-03-17 05:40:19,759] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:40:19,759] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:40:19,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fd0e52d-2e30-40bb-8dc9-b98c47d6439c/dqc_reference/checkm_data
[2023-03-17 05:40:19,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:40:19,765] [INFO] Task started: CheckM
[2023-03-17 05:40:19,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30061/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30061/checkm_input OceanDNA-b30061/checkm_result
[2023-03-17 05:41:15,506] [INFO] Task succeeded: CheckM
[2023-03-17 05:41:15,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:41:15,509] [INFO] ===== Completeness check finished =====
[2023-03-17 05:41:15,509] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:41:15,510] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30061/markers.fasta)
[2023-03-17 05:41:15,511] [INFO] Task started: Blastn
[2023-03-17 05:41:15,511] [INFO] Running command: blastn -query OceanDNA-b30061/markers.fasta -db /var/lib/cwl/stg5fd0e52d-2e30-40bb-8dc9-b98c47d6439c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30061/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:41:16,476] [INFO] Task succeeded: Blastn
[2023-03-17 05:41:16,477] [INFO] Selected 22 target genomes.
[2023-03-17 05:41:16,477] [INFO] Target genome list was writen to OceanDNA-b30061/target_genomes_gtdb.txt
[2023-03-17 05:41:16,655] [INFO] Task started: fastANI
[2023-03-17 05:41:16,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgee03a6a6-3129-419f-a29f-23845e6eeeee/OceanDNA-b30061.fa --refList OceanDNA-b30061/target_genomes_gtdb.txt --output OceanDNA-b30061/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:41:32,478] [INFO] Task succeeded: fastANI
[2023-03-17 05:41:32,490] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:41:32,490] [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_015644665.1	s__Roseobacter sp015644665	77.2569	228	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811755.1	s__Roseobacter cerasinus	77.2305	181	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932215.1	s__Roseobacter ponti	76.9536	211	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154785.2	s__Roseobacter litoralis	76.9347	205	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	76.7953	148	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014337925.1	s__Roseobacter litoralis_A	76.7722	164	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102535.1	s__Sulfitobacter delicatus	76.7445	123	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	76.7263	187	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	76.594	148	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	76.572	175	1179	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_001886735.1	s__Sulfitobacter alexandrii	76.5646	142	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634885.1	s__Sulfitobacter sp001634885	76.5246	139	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
GCA_003511785.1	s__UBA7951 sp003511785	76.3468	77	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172095.1	s__Sulfitobacter indolifex	76.3267	120	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	76.2956	118	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	76.2931	106	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016019955.1	s__Shimia sp016019955	76.2424	112	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	99.56	99.56	0.93	0.93	2	-
GCF_001292625.1	s__Shimia sp001292625	76.0042	82	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054175.1	s__Allosediminivita pacifica	75.9855	76	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Allosediminivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900207575.1	s__Cereibacter_A ovatus	75.9826	63	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811755.1	s__Pararhodobacter sp017811755	75.7925	61	1179	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:41:32,490] [INFO] GTDB search result was written to OceanDNA-b30061/result_gtdb.tsv
[2023-03-17 05:41:32,491] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:41:32,493] [INFO] DFAST_QC result json was written to OceanDNA-b30061/dqc_result.json
[2023-03-17 05:41:32,493] [INFO] DFAST_QC completed!
[2023-03-17 05:41:32,493] [INFO] Total running time: 0h1m51s