[2024-01-24 11:05:24,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,551] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3591ed0-eac8-49a3-969f-cdaff3699935/dqc_reference
[2024-01-24 11:05:26,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,177] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,178] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dcb2ed3-6870-4566-a62c-7f5b197005ae/GCF_003721245.1_ASM372124v1_genomic.fna.gz | prodigal -d GCF_003721245.1_ASM372124v1_genomic.fna/cds.fna -a GCF_003721245.1_ASM372124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:35,040] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:35,040] [INFO] Task started: HMMsearch
[2024-01-24 11:05:35,040] [INFO] Running command: hmmsearch --tblout GCF_003721245.1_ASM372124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3591ed0-eac8-49a3-969f-cdaff3699935/dqc_reference/reference_markers.hmm GCF_003721245.1_ASM372124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:35,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:35,342] [INFO] Found 6/6 markers.
[2024-01-24 11:05:35,374] [INFO] Query marker FASTA was written to GCF_003721245.1_ASM372124v1_genomic.fna/markers.fasta
[2024-01-24 11:05:35,375] [INFO] Task started: Blastn
[2024-01-24 11:05:35,375] [INFO] Running command: blastn -query GCF_003721245.1_ASM372124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3591ed0-eac8-49a3-969f-cdaff3699935/dqc_reference/reference_markers.fasta -out GCF_003721245.1_ASM372124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:36,065] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:36,068] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:36,069] [INFO] Target genome list was writen to GCF_003721245.1_ASM372124v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:36,078] [INFO] Task started: fastANI
[2024-01-24 11:05:36,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dcb2ed3-6870-4566-a62c-7f5b197005ae/GCF_003721245.1_ASM372124v1_genomic.fna.gz --refList GCF_003721245.1_ASM372124v1_genomic.fna/target_genomes.txt --output GCF_003721245.1_ASM372124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:47,252] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:47,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3591ed0-eac8-49a3-969f-cdaff3699935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:47,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3591ed0-eac8-49a3-969f-cdaff3699935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:47,267] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:47,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:47,268] [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
Marinomonas hwangdonensis	strain=HDW-15	GCA_003721245.1	1053647	1053647	type	True	100.0	1137	1139	95	conclusive
Marinomonas arctica	strain=CGMCC 1.6498	GCA_014645175.1	383750	383750	type	True	83.5024	635	1139	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	83.48	647	1139	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	82.0004	654	1139	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	81.4399	604	1139	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	81.348	604	1139	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	80.7473	535	1139	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_020694005.1	2726122	2726122	type	True	80.6555	584	1139	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_012584435.1	2726122	2726122	type	True	80.638	563	1139	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	79.9079	477	1139	95	below_threshold
Marinomonas profundimaris	strain=D104	GCA_000508165.1	1208321	1208321	type	True	79.7114	480	1139	95	below_threshold
Marinomonas flavescens	strain=ANRC-JHZ47	GCA_004352835.1	2529379	2529379	type	True	78.9754	270	1139	95	below_threshold
Marinomonas colpomeniae	strain=SM2066	GCA_014803385.1	2774408	2774408	type	True	78.7667	343	1139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:47,269] [INFO] DFAST Taxonomy check result was written to GCF_003721245.1_ASM372124v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:47,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:47,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:47,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3591ed0-eac8-49a3-969f-cdaff3699935/dqc_reference/checkm_data
[2024-01-24 11:05:47,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:47,310] [INFO] Task started: CheckM
[2024-01-24 11:05:47,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003721245.1_ASM372124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003721245.1_ASM372124v1_genomic.fna/checkm_input GCF_003721245.1_ASM372124v1_genomic.fna/checkm_result
[2024-01-24 11:06:18,426] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:18,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:18,447] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:18,448] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:18,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003721245.1_ASM372124v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:18,449] [INFO] Task started: Blastn
[2024-01-24 11:06:18,449] [INFO] Running command: blastn -query GCF_003721245.1_ASM372124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3591ed0-eac8-49a3-969f-cdaff3699935/dqc_reference/reference_markers_gtdb.fasta -out GCF_003721245.1_ASM372124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:19,519] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:19,524] [INFO] Selected 15 target genomes.
[2024-01-24 11:06:19,524] [INFO] Target genome list was writen to GCF_003721245.1_ASM372124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:19,536] [INFO] Task started: fastANI
[2024-01-24 11:06:19,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dcb2ed3-6870-4566-a62c-7f5b197005ae/GCF_003721245.1_ASM372124v1_genomic.fna.gz --refList GCF_003721245.1_ASM372124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003721245.1_ASM372124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:30,916] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:30,927] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:30,928] [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_003721245.1	s__Marinomonas hwangdonensis	100.0	1137	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003259225.1	s__Marinomonas arctica	83.4524	649	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900129155.1	s__Marinomonas polaris	81.9985	654	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_003259175.1	s__Marinomonas shanghaiensis	81.4286	605	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018336955.1	s__Marinomonas sp018336955	81.3276	605	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017285.1	s__Marinomonas sp000017285	81.1541	601	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_003337275.1	s__Marinomonas foliarum	80.7592	534	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_012584435.1	s__Marinomonas sp012584435	80.6215	564	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018336975.1	s__Marinomonas sp013373235	80.3025	528	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.11	98.11	0.83	0.83	2	-
GCF_003315485.1	s__Marinomonas rhizomae	80.2881	549	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013372285.1	s__Marinomonas primoryensis	79.9278	474	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	-
GCF_008122525.1	s__Marinomonas sp008122525	79.6784	427	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521805.1	s__Marinomonas ushuaiensis	79.119	353	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352835.1	s__Marinomonas sp004352835	78.9754	270	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314975.1	s__Marinomonas aquiplantarum	78.8957	317	1139	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:30,929] [INFO] GTDB search result was written to GCF_003721245.1_ASM372124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:30,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:30,943] [INFO] DFAST_QC result json was written to GCF_003721245.1_ASM372124v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:30,943] [INFO] DFAST_QC completed!
[2024-01-24 11:06:30,944] [INFO] Total running time: 0h1m6s