[2023-03-16 19:57:56,503] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:57:56,503] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:57:56,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b0d1483-c811-4997-8ff8-ebf1b6d75e29/dqc_reference
[2023-03-16 19:57:57,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:57:57,624] [INFO] Task started: Prodigal
[2023-03-16 19:57:57,624] [INFO] Running command: cat /var/lib/cwl/stgec106ad9-432f-449b-9e83-dae39341193e/OceanDNA-b36120.fa | prodigal -d OceanDNA-b36120/cds.fna -a OceanDNA-b36120/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:58:17,060] [INFO] Task succeeded: Prodigal
[2023-03-16 19:58:17,060] [INFO] Task started: HMMsearch
[2023-03-16 19:58:17,060] [INFO] Running command: hmmsearch --tblout OceanDNA-b36120/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b0d1483-c811-4997-8ff8-ebf1b6d75e29/dqc_reference/reference_markers.hmm OceanDNA-b36120/protein.faa > /dev/null
[2023-03-16 19:58:17,250] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:58:17,251] [INFO] Found 6/6 markers.
[2023-03-16 19:58:17,270] [INFO] Query marker FASTA was written to OceanDNA-b36120/markers.fasta
[2023-03-16 19:58:17,270] [INFO] Task started: Blastn
[2023-03-16 19:58:17,271] [INFO] Running command: blastn -query OceanDNA-b36120/markers.fasta -db /var/lib/cwl/stg5b0d1483-c811-4997-8ff8-ebf1b6d75e29/dqc_reference/reference_markers.fasta -out OceanDNA-b36120/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:58:18,049] [INFO] Task succeeded: Blastn
[2023-03-16 19:58:18,050] [INFO] Selected 26 target genomes.
[2023-03-16 19:58:18,051] [INFO] Target genome list was writen to OceanDNA-b36120/target_genomes.txt
[2023-03-16 19:58:18,067] [INFO] Task started: fastANI
[2023-03-16 19:58:18,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgec106ad9-432f-449b-9e83-dae39341193e/OceanDNA-b36120.fa --refList OceanDNA-b36120/target_genomes.txt --output OceanDNA-b36120/fastani_result.tsv --threads 1
[2023-03-16 19:58:34,557] [INFO] Task succeeded: fastANI
[2023-03-16 19:58:34,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b0d1483-c811-4997-8ff8-ebf1b6d75e29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:58:34,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b0d1483-c811-4997-8ff8-ebf1b6d75e29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:58:34,572] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:58:34,572] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:58:34,573] [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
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	82.424	673	995	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	79.0504	350	995	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	77.8234	326	995	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	77.6432	275	995	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	77.5551	292	995	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	77.4602	280	995	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	77.4063	250	995	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	77.3554	215	995	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	77.2669	247	995	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	77.2604	219	995	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	76.7804	186	995	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	76.7544	145	995	95	below_threshold
Xanthomonas citri	strain=LMG 941	GCA_000263335.1	346	346	pathovar	True	76.5776	118	995	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	76.4057	137	995	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.3251	124	995	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	76.3112	148	995	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2878	140	995	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	76.2713	136	995	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.2215	147	995	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	76.1374	152	995	95	below_threshold
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	76.0981	116	995	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.0721	109	995	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	76.0218	144	995	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	76.0086	142	995	95	below_threshold
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	76.007	78	995	95	below_threshold
Xanthomonas citri	strain=CFBP 2526	GCA_000495275.1	346	346	pathovar	True	75.9794	105	995	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:58:34,573] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36120/tc_result.tsv
[2023-03-16 19:58:34,573] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:58:34,573] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:58:34,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b0d1483-c811-4997-8ff8-ebf1b6d75e29/dqc_reference/checkm_data
[2023-03-16 19:58:34,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:58:34,591] [INFO] Task started: CheckM
[2023-03-16 19:58:34,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36120/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36120/checkm_input OceanDNA-b36120/checkm_result
[2023-03-16 19:59:39,481] [INFO] Task succeeded: CheckM
[2023-03-16 19:59:39,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:59:39,487] [INFO] ===== Completeness check finished =====
[2023-03-16 19:59:39,487] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:59:39,488] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36120/markers.fasta)
[2023-03-16 19:59:39,490] [INFO] Task started: Blastn
[2023-03-16 19:59:39,490] [INFO] Running command: blastn -query OceanDNA-b36120/markers.fasta -db /var/lib/cwl/stg5b0d1483-c811-4997-8ff8-ebf1b6d75e29/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36120/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:59:41,125] [INFO] Task succeeded: Blastn
[2023-03-16 19:59:41,127] [INFO] Selected 17 target genomes.
[2023-03-16 19:59:41,128] [INFO] Target genome list was writen to OceanDNA-b36120/target_genomes_gtdb.txt
[2023-03-16 19:59:41,148] [INFO] Task started: fastANI
[2023-03-16 19:59:41,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgec106ad9-432f-449b-9e83-dae39341193e/OceanDNA-b36120.fa --refList OceanDNA-b36120/target_genomes_gtdb.txt --output OceanDNA-b36120/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:00:00,622] [INFO] Task succeeded: fastANI
[2023-03-16 20:00:00,632] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:00:00,633] [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_002706265.1	s__Polycyclovorans sp002706265	99.962	965	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	99.22	98.54	0.87	0.78	3	conclusive
GCF_000711245.1	s__Polycyclovorans algicola	82.4356	672	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016918765.1	s__Polycyclovorans sp016918765	79.0613	350	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	77.8078	325	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	77.7946	258	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297005.1	s__Stagnimonas sp004297005	77.7493	251	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
GCF_003428335.1	s__Solimonas_A sp003428335	77.7368	318	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	77.6889	291	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	77.6065	289	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	77.4311	283	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	77.3685	214	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	77.2675	247	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305095.1	s__Thermomonas sp017305095	76.7821	137	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733765.1	s__Algiphilus aromaticivorans	76.7804	186	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Algiphilaceae;g__Algiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003505795.1	s__UBA8801 sp003505795	76.2478	114	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__UBA8801	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467105.1	s__Pseudomonas_E alcaligenes	76.0265	145	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_014199795.1	s__Xanthomonas_A sp014199795	76.0126	173	995	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.20	98.15	0.95	0.95	4	-
--------------------------------------------------------------------------------
[2023-03-16 20:00:00,634] [INFO] GTDB search result was written to OceanDNA-b36120/result_gtdb.tsv
[2023-03-16 20:00:00,634] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:00:00,637] [INFO] DFAST_QC result json was written to OceanDNA-b36120/dqc_result.json
[2023-03-16 20:00:00,637] [INFO] DFAST_QC completed!
[2023-03-16 20:00:00,637] [INFO] Total running time: 0h2m4s